Home

Manual for beginners (pdf: 2.73 MB)

1. ElSerine Glycine and c 2 Keto 3 methylvalerate 2 D threao Hydroxy 3 carboxy isocaproate 2 Keto 4 metylpentancate l HHistidine and nucleic amp lMiscellaneous amino prepiri aE acid aminotransferase QO O Branched chain aminc acid aminotransferase O O O Bi pids metabolism r ENIE ENERSEN PEE FE SE E T F Then select the data as in the figure below and click the Update Correlation button Unioooos 2008 03 28 L Leaucine L Isolaucine eS A Leucine Valine and assess s s s isoleucine metabolism _ ns 22 4 Data Analysis Advanced Correlation Line Correlation Gene Ath ATTED ll AthGeneCor v3 1388 chips gt 0 6 Compound Demo data from time course exps of drug treated Ath cells Update Correlation Smooth lines are appeared on the pathway map These lines indicate the relationships between the genes red and between the metabolites green Leucine valine isoleucine and alanine biosynthesi Ta Lysine threonine anc Glycolysis methionine biosynthesis Katol acid reductoisomerase Acatolactate synthase Threcnine dehydratase 2 Oxobutancate 2 3 Dihydroxy isovalerate FR emits Go Dihydroxyacid j USRS SRS NN T X 3 Isopropyimalate dehydratase 2 D threo Hydroxy 3 carboxy isocaproate Branched chain amino acid aminotransferase Leucine Valine and isoleucine metabol
2. DB transcnpty 2 2 The Main Menu After logging in you can see the main window Tampir Upload You can upload your nan cata expedest daca map date and conelation tna tor anabypses Other users PEAR aboeed po OES DI Them Alber kangi learns frome KP A level gts of cloang the brawder af the eploadiad dita are 1o b deleted bom fie nirai Oni he deta of he dia brna pled look ot thee tanpa Gilad Steeple File Dowriiai lunalved Voy Can Create fevers gapir bea here ts view the dita on the mbabe pdb rung Map Wiew AA he malibot paltry mapi can be Di m ftom bere Sanarch Geren metacoltes aed eyes inataled in aPC A Ven ane nearchebles anc you can check whai mebabolc mapa they are diwan on or soma SPRES bizi geernch meequance tewecdory peach in lab ioe Dhcewevboad Al the aqpenvent cre you alee to mee and the oraban thes that the KPPA pyram os refemeg can be doerdioaded tom tere Copri 0 200d Kruse DMA Research bnehdute Al Paghis Asser On the top of the window the main menu is placed C KaPPA View4 Manual for Beginners Main Temporary Upload Analysis Map View search Download e Main Returns to the main window e Temporary Upload Uploading your experimental data User Map data and correlation data for your analyses is operated through this menu All the uploaded data is going to be deleted completely after you are logging out e Analysis Uploaded data is displayed on the pathway maps through this menu It serv
3. Ribulose 1 5 bisphosphate Aldolase phoephate Phogphcribulckinage D Fructose 1 6 5 phoephate bisphosphate D Ribulose 5 phoephate Fructose bisphosphatase D Ribulose 5 phosphate 3 apimerase D Erythroee 4 phosphate To switch the Compared Experiment Pair click on Ath 2 The window will be redrawn with the data of Ath 2 and you will find Ath 2 is checked 22 Compared Experiments C Ath 1 Ath 2 Ath 2 Transcript Sample Ath C Sample Ath D Calvin cycle Phosphoglycerate kinase 3 Phcepho 3 Phoepho D glyceroyl D glycerate Glycolate pathway ep O ceo phoephate Gluconeogenesis Triceephosphate isomerase Glycaraldehyde 3 hate OO Glyceraldehyde 3 phcephate dehydrogenase Ribulcee bisphog carboxylase small Dihydroxyacetone phoephate yarog NADP phoephorylating hate subunit E m Carbon dicxide Carbon dioxid D Ribulose A P Transketolase pide ra 1 5 bisphosphate pho ephate Phosphoribulokinase D Xylulose 5 phoephate C D Fructose 1 8 o bisphosphate Fructoee bisphosphatase D Ribulose 5 phosphate 3 apimerase D Erythrose 4 phosphate Because metabolite experiments were not included in the Compared map Show All Experiments KaPPA View4 Manual for Beginners Experiment Pair Ath 2 the symbols for the me
4. When the Universal is selected Universal Map Mode the information of all the species is displayed on the pathway maps You can see the differences of the gene assignment to the enzyme reactions between the species Citrate synthase s a Aconitase hydratase OOOO 5 oO sly OO osa OO oss oOo0000 ah Citrate OOO ath Gs Aconitate Aconitase hydratase o HHo EE e _ isocitrate lyase beta Oxidation of saturated fatty acic COA Glyoxylate Succinate When there was not an enough space on the map to represent all the gene assignment a box written as will appear Clicking on the box a pop up box is displayed to view the all n ro 5 Other Functions eT Citrate synthase Acalyl CoA ce Aconitasa hydratase ath O Lja O 3 os Doo cis Aconitate sy O isocitrete lyase The species displayed on the pathway maps could be changed by the user by clicking the Select Species button at the bottom of the map Ribose 5 phosphate isomerase Glyceraldeh phoephate D Ribose 5 phosphate o D 3 Uni00112 20080375 pha Transketolase Select Species Element List Download Plz A pop up window will be displayed Check on the species you would like to display on the maps and press the Submit button and then Redraw button to refresh the map on the main window 2 Kal TA Wiel pecias Select Wnjoss CL S 1 4 m ji l F a r y r RAREN BS OT ee A
5. alanine biosynthesis _ O Lysine threonine anc Glycolysis methionine biosynthesis a Katol acid reductoisomerase Acatolacate synthase Threonine dehydratase 3 2 Oxobutanoate 2 3 Dihydroxy isovalerate L Threonine O 2 Acatolactate Dihydroxyacid o dehydratase Branched chain amino Acatolactate synthase acid aminotransferase Alanine aminotransferase 2 Aceto 2 hydroxybutyrate BORTHEN Lins 2 Ketoisovalerate Katol acid reductoisomerase 2 lsopropyimalate 2 3 Dihydroxy 3 methylvalerate D 3 lsopropyimalate Dihydroxyacid dehydratase dehydratase 2 Kato 3 methylvalerate 2 D threo Hydrony yv 3 carboxy isocaproate dy Branched chain aminc Branched chain amino acid aminotransferase acid aminotransferase QS ee Leucine Valine and L isoleucine ane L teucine Qe occce wae Torre UNIDOS 2006 05 26 gt isoleucine metabolism V In this figure three red lines are drawn However three gene symbols on the left hand side are for the same gene As shown here by setting a number in the Number field users can filter the correlation data to display the lines of highest values in the restricted range When you would like to view the correlation lines of the lowest values in the range select Low from the pull down list Range Number maf 3 0 6 6 0 9 71 0 4 1 3 Details of the Correlation Data Displayed You can see what
6. button then a pop up window will appear Sedoheptulose bisphosphatase OO O D Ribose 5 phosphate D Sedoheptulose 7 Uni00112 2008 035 phcephste Transketolase Aas ited ap When Universal is selected the button is not displayed o 3 4 Data Analysis Advanced In the pop up window you can set a combination of the maps In the Multiple Map Mode top left panel of the tiled maps is automatically set to the one which is currently viewed selected in the pathway tree of the main window Therefore Current Map is written in the top left panel and you would select here the other 3 maps 1 e top right bottom left and bottom right panels By clicking a map name in the pathway tree of the pop up window thumbnail of the map will be added to the preview area sequentially in the order above Plant metabolic pathways Multiple Map Create Carbohydrate metaboli Amino acid nucleic ac 1 ipids metabolism soprenoid metabolism Phenylpropanoid and s Gene families and mis Functional categories Current Map A iv Clear Clear You don t have to select all of 3 maps Selection of only one or two maps is acceptable After selecting the maps enter a name of the combination in the Name field and click the Add button Asa Redraw Next click the Redraw button to refresh the main window After that close the pop up window A pull down list of Multiple Map will
7. genes and metabolites are connected by lines in the current map and what the correlation values are by clicking the Correlation List Bo KaPPA View4 Manual for Beginners Element List Correlation Li thy Histogram Color Legend Download Plain Map Print Map Alternatively when the mouse cursor is over the correlation lines the lines are highlighted and the gene IDs and the correlation values are shown in a tool tip COxobutnoete L Threonine 4 1 4 Displaying densities of the Correlation Lines on the Bird s Eye maps When the Correlation is selected for Display Mode in the Bird s Eye Map users can see the line numbers on the pathway maps Correlation iia Display Mode In the similar way described above please select the data to view and the filter conditions at the bottom panel 4 Data Analysis Advanced Amino acid nucleic acid and nitrogen containing derivative metabolism F Histidine and nucleic acid metabolism Aromatic amino acid metabolism Vor E a 0106 C Aspartate and related amino acid metabolism 120s E 27s a es ee 0 Ga oe ba a po ne EEE FR rrr G ons C _ 08 Co G a 121 a 116 Ga we on2 C _ N T4107 E M 26 t ar C m 0 5 C 7 13 200 M ote T s _ mom Cc T 01 C M07 Cc i T SN MM 012 Gluccsinolate metabolis F Tana Mss Qos 7 mor CD _ 7 13 So ou on 7 15 E 445 x
8. in the sample data represents the version number Then click the Upload button Following window will be displayed to check the data Expanment eer Map Correlation Expenmernt File E1 Experiment Type Transenpt O Metabole Paray Typi Sahi e Expenment Narve Repetition Humber Comment Sample Ath sample Ath E 1 1 Sample Mh C 1 2 Sample Ath O 1 2 1 Sample All Zero Control The file contains DNA microarray data of Arabidopsis Each of the data named Sample Ath A and P is from a single experiment C and D contain Be KaPPA View4 Manual for Beginners experimental duplications In addition a dummy data Sample All Zero Control is included in the file As mentioned above this data is obtained from Arabidopsis So select an Arabidopsis thaliana AGI codes from the Array Type pull down list Select H ni otus japonicus Ag Oryza sativa Agilent G4138A Oryza sativa AK Solanum lycopersicum Press the Submit button to start uploading and registration the data to KaPPA View4 server After completing the process you can see the following message It takes a few tens of seconds The operation succeeded 2 4 2 Uploading of Metabolite Data Here we demonstrate the way to upload a metabolite data file It is similar to the case of DNA microarry data 2 4 1 Click the Temporary Upload from the main menu and select a file named
9. maps prepared by themselves k KaPPA View4 Manual for Beginners The GS GOGAT Cycle fence r jE T pe ame a a Soo Peer etree ee erry J oe i pe C i i a yes _ ma e Sinj eo al The ERETTE T Cpele dromabt mec iced rra maj miee ut mee i i o m ESF y i lt lt E7 CCN B ime Ho bo s a Goa y O a SAEN ANGT fF a es el Se gts Tk ae 7 a e ie a o O a a E a Ti Sr o gt in fee FS m r L aaa ee Furthermore gene to gene and or metabolite to metabolite relationships such as co expression correlations of genes can be displayed on the maps This is the distinctive feature of KaPPA View and will help you for example to analyze the relationships between metabolic genes and transcription factors that control their expressions T ae 5 be i pi any O H bf 2 amp SS AS i KaPPA View4 can handle multiple species and genes of several species can be displayed side by side on the maps The system also provides functions to upload and view the omics data from external applications n Te 1 Introduction 1 2 Downloading Sample Data This manual guides practical operations of the system using sample data sampleFiles zip which is available from the top page of KaPPA View4 http kpv kazusa or jp kpv4 or form the main window displayed just after logging in KaPPA View 4 As the file is compress
10. page v PI Calvin cycle El Arabidopsis thaliana metab Click Create Simple Map button appeared under the pathway map tree Arabidopsis thaliana Carbohydrate metabolisr ECO fixation and cent Calvin cycle Gluconeogenesis kinase f i 50 Calvin cycle arpa 3 Phoepho D glyceroyi Glycaraldehyde Tricsephospheta isomerase glycarate hcephat 3 phosphate a doo Pheeehate e B Glycolate pathw Glycolate pathway C o e o m m 2 Dihydroxyacato 3 a Glyceraldehyde 3 phosphate phoephate Glycolysis glucc dehydrogenase NADP phoephorylating B Phosphoenolpyr Ribulcee bisphosphate carboxylase small subunit f MA TCA cycle E Glyoxylate cycle Fructose bisphosphate Glycerol metabc D Ribulose aldolase Aldolase D Fructose 6 Atmosphere phoephate 1 5 bisphosphate lMono di and oligos Hoota Oz osphcribulckinase Polysaccharide metal Xylulose 5 phoephate Miscellaneous carboh D Fructose 1 6 bisphosphate D Ribulose 5 Amino acid nucleic acid pa i 2 Fruct e bisphosphatase Create Simple Map D Ribulose 5 phosphate 3 apimerase D Erythroee 4 phosphate Ribose 5 phosphate O isomerase 0o npo 0 Fructose bisohosohatase aldolase When Universal is selected the button is not
11. to the information page of the genes metabolites enzymatic reactions and pathway maps in KaPPA View4 After jumping the user will be recognized as a guest user and he she can continue to browse and analyze data with KaPPA View4 http kpv kazusa or jp kpv4 geneInformation view action id At1 58150 http kpv kazusa or jp kpv4 compoundInformation view action id KPC00697 http kpv kazusa or j p kpv4 enzymelInformation view action id R0000603 http kpv kazusa or jp kpv4 map View view action mapNumber 00006 The species can be specified too http kpv kazusa or jp kpv4 geneInformation view action id At12g58150 amp spec 1iesName Arabidopsis thaliana You can check this action with a file ExampleUrlLink v html in the URL_link folder of sample data Please open the file with the Internet browser 5 3 2 POST Data Transferring Function This function is provided for developers of database sites and application programs where microarray and metabolome data are deposited In the usual way to represent the omics data on the pathway maps with KaPPA View4 users have to login to the system and upload data files through the KaPPA View4 web user interfaces The POST data transferring function POST function provides logging in and data uploading environments through computational procedures without user s manual operation Therefore the developers can place for example View buttons in their database sites to view the data directl
12. 202 Experiment Value ID Color Ratio Sample Ath C Sample Ath D At3g12780 E a 0 9159 0 148 0 7678 1 467 0 978 0 489 0 000 0 489 0 978 1 467 Ath 1 Ath 2 linear 2 log Ratio V show symbol 3 3 The Bird s Eye Map We described so far about the pathway maps placed at the lowest tier leaf of the Pathway Tree Now please click the middle tier of the tree branch Following map will appear 24 KaPPA View4 Manual for Beginners Arabidopsis thaliana zl Amino acid nucleic acid and nitrogen containing derivative metabolism ElArabidopsis thaliana metabus View Thumb Nails View Birds Eye Map Display Mode Name gt Select Aspartate and related Glutamate and related Leucine valine isoley Amino acid nucleic acid and nitrogen containing Glucosinolate metabo derivative metabolism a Aromatic amino acid 1 Histid d eic acid metabolism Serine Glycine and c sare mdd raiak Histidine and nucleic i i Aromatic amino aci id biosynthesis ui sis Miscellaneous amino Purine nestle jpids metabolism Tyrosine metabolism soprenoid metabolism Phenylpropanoid and shi Gene families and misce al gt Fomyl THF biosynthesis These maps are called Bird s Eye map in KaPPA View4 Each of all the pathway maps included in the branch is represented as bar indicator bar At the first time to display Bird
13. 8554 0 5 Ati g01030 1 118873492 1 41118869 1 26662646 1 29633266 0 01673949 0 06297865 0 6 Ati g01040 1 21811202 0 96145002 0 07469906 011324618 1 086869507 1 064449577 0 7 At1g01050 0 66493581 0126151787 1 175051608 1 170206475 0529977397 040708899 0 8 Ati gO1060 0809261597 1 566740565 0579037425 O6o09907787 1 405337658 1 391461944 0 9 Atig01070 1 20441321 088953735 061000164 0611701704 1 334508091 1 361604332 0 10 Ati gO10B0 0904213049 1 059304533 0 07728201 0 060123451 062478665 0 6922613 0 11 Ati 01090 1 467257461 0 322397127 0615823494 05186919149 0 99989596 099000439 0 12 AtigO1100 1 285759095 0 0542067 0 33525193 039955302 O756790904 0754720246 0 13 Attg01110 0 57385919 03863093021 1 06143081 1 24032402 0 661393 0 55626915 0 Fig 2 5 1 Sample_Ath_gene_v csv A B C D E E G H 1 compexp Sample Ath A Sample Ath B Sample Ath B Sample Ath C Sample Ath C Sample All 1 Control 2 rep 1 1 2 1 2 1 3 KPCOO00 657 124 125 5 29839 5 34677 1 4 KPCOO002 9 9967 10274 0 0009 0 0009 1 5 KPCOOO0S 241184 664 664 279 14815 275 60648 1 6 KPCOO004 122 16 18 6 77778 6 66667 1 7 KPCOO005 5140 372 arr 13 81 72 13 51075 1 8 KPCOQOQG 463 51 51 9 07843 9 39216 1 9 KPCOO0O0 7 458 4281 22 436831 0 001 07 0 001 OF 1 10 KPCOO00S 50484 752 772 67 13298 66 69149 1 11 KPCOOOOS 53 235794 238191 0 00022 0 00022 1 12 KPCO0010 64323 890 696 72 27303 72 54719 1 13 KPCOO01 1 91 1299 1294 0 07005 0 07159 1 Fig 2 5 2 Sample_Ath_met_v
14. Far AA e y asl KaPPA View4 Manual for Beginners In the Universal Map Mode you can compare omics data between the species too When you set more than two Compared Experiment Sets originated from way map Click the button Ath Data Compad Eaparinents Ath Data several species an extra button Show All will be displayed on the top right of the path aly Data Ath Data Tranecripa sample Al Leaves 21 days sample _A2 TE cultured cells 14 days Metabolite Kazusa TS GewihCune day 017 Kazusa TAT GrewthCune day 02 Calvin cycle pee Pheaphegeania Ghuconeogencsis bra a a d Phea 2 Phasa giomi irakaj A Trepp Sc Tee A F q orrei anes pheeshune oa bphoaphate 2 Ghyeninin pathwmy fp ohonnlehyde 2 phrasi d a delr NED j pheapherjatrg pJ Ribuioss Siaphanphans OEO ud oun Giyanto wh Compared Experiments You can select one data from each species and click Submit button Ath Datat Sly Data Ath Data Arabidopsis thaliana Solanum lycopersicum Sly Data accumulations on a single pathway map Then you get the comparative visualization of gene expressions and metabolite On Calvin cycle Phosphoglycerate ki unase 3 Phoe p apo Bapo o2 3 Pho pho D glyceroyi a y DDMA t phcephate Glycolate pathway P Triceephosphate isomerase Glyceraldehyde Pnoep mm S phosphate GH os O Da ih Dihydroxyaceton
15. KaPPA View Kazusa Plant Pathway Viewer KaPPA View 4 The Kazusa Plant Pathway Viewer Version 4 0 Manual for Beginners ver 1 2 ee Kazusa DNA Research Institute Table of Contents Table of Contents Mi MIU OC UICUIO p snes ccs emcees casein ce ceed weet one asc E A cen sede sey enwed sen savexseaeeneye 1 1 1 Overview Of KaPPA ViICW4 cccccccssesesseseeeeeeeeeeeesseeeeeeeeeseaassaseeeeeeseaaaseeeeeeeennaas 1 1 2 Downloading Sample Datta cccccccccccecceccceeeseeeseeceeeeeeseeeeeeeeeeeeeesssaseeeeeeeeessaaaaeess 4 Des NSF NO erin oen r EE EN E A O E E EE 4 1 4 Other MANuals cccccccccccccccseeeeeessseeeeeeeeeeeeeeeeeeeeeaaeeaaaaaaaaeeeeeeeeeeeeeeeseeaaeaaaaaaasseesees 5 2 Starting the Analysis Login and Upload of Experimental Data 6 2 Nie Eo ea E E E A E E A 6 2 2 Ne Main Men sciana RATARA ERR 6 e LOO aE E E E E EE 7 2 4 Uploading Experimental Data ccccccesccccsseeeeceeeeeeeceeeeeesaeeeeesseesseeesseeeesneeesensaes 8 2 4 1 Uploading of DNA microarray data ccccccccccseeeeeeeeseeeeeeeeeeeeeeeesaeeseeeseeeaeeeesssaeeeeseaenes 8 2 4 2 Uploading of Metabolite Data cc cecccccccssseeceeeeeeeeeeeeeaeeeeesseeeeceeeeseeeeeeesaeeeeeeessaeeeeeeeas 9 2 5 File Format of the Experiment Data ccccccccecssseeeeseeseeeeeeeeeeeeeeeeeseaeeeeesaeeeeeas 10 3 Data Analysis Basic ccccessccsseecsseseseeneesesesenseeenssensenesee
16. KaPPA View4 Manual for Beginners Create New Account Login Name Email Submit An e mail will be sent to you immediately and it informs you the access password 6 2 Expiration of the Power User The Power User account will be automatically deleted in 30 days after latest logging in All the data uploaded by the Power User will be deleted too An alert e mail will be sent to you in 21 days after last login To keep your account please login again before the expiration date 6 3 Power User Login Enter your name and password in the fields on the top page and then press the Login button KaPPA View 4 Kazusa Plant Pathway Viewer Home Overview News Statistics Download Link Publication Contributor About Us Login Welcome to KaPPA View4 Classic Go to My Page Name jusemame Enter Password eccccccces Please click the button to start All the data is freely accessible for publi Login users More advanced you can save your own data on KaPPA View4 by creating your account Enter and click Create Account for an immediats registration free Gene information for Oryza sativa was changed August 15 2010 The transcript IDs from RAP DB have been used for gene IDs of Oryza sativa We changed the gene IDs of it to the locus IDs from RAP DB so that the correlation data of rice could be represented The old settings are preserved as the species name Oryza sativa RAP DB transcript so your micr
17. One metabolite to metabolite co accumulation data calculated from a series of metabolomics data obtained from a drug treated Arabidopsis cultured cells in our laboratory is also available as a demonstration data Let s try the operation As an example please select a metabolic map Leucine valine isoleucine and alanine biosynthesis of Arabidopsis thaliana Arabidopsis thaliana i 4 Leucine valine isoleucine and alanine biosynthesis fC gt s 3 o e Lysine threonine anc El Arabidopsis thaliana metab Glycolysis methionine biosynthesis 7 aaaaaaaaaaaaa EEE Er E A Acatoladate synthase Threcnine dehydratase a Carbohydrate metabolisr aa j 2 Oxobutancete 2 3 Dihydroxy isovalerate L Threonine El Amino acid nucleic acid o Dihydroxyacid dehydratase 2 Acatolactate El Aspartate and related amp hGlutamate and relatec A l y Branched chain amino Acatolacdate synthase acid aminotransferase Alanine aminotransferase SOGOGEED ine 2 Aceto 2 hydroxybutyrate ElGlucosinolate metabo i 2 Ketoisovalerate ElLeucine valine isoleu L Alanine ee aad recucivisomersase 2 lsopropyimalate Leucine valine TE 2 3 Dihydroxy 3 methylvalerate Leucine valine z 3 Carboxy S hydroxyisocaproate o 3 lsopropyimalate Dihydroxyacid dehydratase dehydratase 3 lsopropyimalate dehydrogenase ElAromatic amino acid i
18. Power Users who uploads a lot of data files with managed header information see Advanced Manual 3 2 Data browsing on the maps Using the data registered in the previous section let s browse the data First of all please select Arabidopsis thaliana from the pull down list on the top left Carbohydrate metabolisr Arabidopsis thaliana Amino acid nucleic acid 1 Select a name of species or Universal from the pt Lipids metabolism 2 Click on a map or a map category on the metabolic REA UEW EU soprenoid metabolism 2Phenylpropanoid and shi Lotus japonicus Gene families and misce Oryza sativa Functional categories Solanum h COp ersicum 11 ipids metabolism 4 lenmrannin matahnaliem Next select one of pathway maps in the metabolic pathway tree An example selecting Calvin cycle is shown here Symbols on the pathway maps are painted in color according to the data ns co 3 Data Analysis Basic Arabidopsis thaliana x Calvin cycle El Arabidopsis thaliana metabl amp Compared Experiments Al AS metabolisr f tz l M Athi O Ath2 T Calvin cycle Glycolate pathw Ath 1 Glycolysis glucq Show All Experiments Transcript Sample Ath A Sample Ath B E Phosphoenolpyr Metabolite Sample Ath A Sample Ath B 7 J EITCA cycle y E Glyoxylate cycle Calvin cycle Phosphoglycerate E Glycerol metabc i amp H Mo
19. SSS S55 Leucine valine isoleucine and alanine metabolism 1 26 v eu5 E C100 ES ws LD The numbers written beside T or M numerators show the numbers of the correlation lines on the pathway maps The numbers after the slashes denominators indicate the numbers of the genes or metabolites drawn on the maps For the indicators of the middle tiers both of the numerators and the denominators are the sum of the line and element numbers included under the tier The color of the bar is decided as follows When defined D logio line number element number of a map Dmax The maximum value of D among the maps under the current tier and Dmin The minimum value of D among the maps under the current tier the bar of the map having Dmax is painted in the strongest color red and the map of Dmin is painted in the weakest color green Therefore the maps having dense relationships are painted stronger colors Correlations calculated in an element self correlations are excluded from the line number counting even if they are included in the uploaded files 4 1 5 Uploading Users Own Correlation Data Users can upload their own correlation data to KaPPA View4 and utilize them in the analysis gat KaPPA View4 Manual for Beginners Click Temporary Upload on the Main menu and select Correlation tab Experiment User Mag Correlation Type Gene Compound Corelation Fie O0 A N
20. Sample _Ath_met_v csv in the data_metabolome folder in the sample data Temporary Upload Experiment User Map Correlation Experiment File g Upload 2 Starting the Analysis The following window will open after clicking the Upload button Eii As this sample data is obtained from Arabidopsis select Arabidopsis thaliana from the Species pull down list In actual the sample data was generated by computational calculation and it did not contain experimental data of the real world Experiment Type Transcript Metabolite Species Select Experiment Nam Select __________ Arabidopsis thaliana yl Solanum lycopersicum The Experiment Type is automatically set to Metabolite by the auto recognition of the file format Then press the Submit button Uploading will be finish with the following message The operation succeeded 2 5 File Format of the Experiment Data Here we show the file format of the experiment data Please try to open the files uploaded in the section 2 4 with Microsoft Excel KaPPA View4 Manual for Beginners A B C D Z F G H I 1 arrayexp Sample Ath A Sample Ath B Sample AthC Sample AthC Sample Ath D Sample Ath D Sample All Zero Control 2 rep 1 1 1 2 1 2 1 3 Ati g01010 0 82847516 0646901298 1 19048388 1 07724172 1 15233451 1 01085621 0 4 Atig01020 1 32244998 0 52495562 016694342 022203733 1 269603413 1 95282
21. ame Comment PO SR Upload Here let s upload a sample data The sample data can be downloaded from the top page of the KaPPA View4 Press the Browse button and select a file named Correlation_Ath_Gene_v csv in the correlation folder in the sample data Input a short description of this file as Upload Test into the Name field The Comment field can be left as blank Press the Upload button After waiting for a while the uploading process will finish with the following message The operation succeeded The data uploaded here can be seen in the pull down menu of the correlation data Correlation Line Correlation Color Gene Upload Test RED No Lines Compound Ath ATTED I AthGeneCor_v3 1388 chips GREET Ath ATTED I AthGeneCor_v3 1386 chips Ath ATTED Il AthGeneCor_v3 1368 chips 4 Ath ATTED I hormones 236 chips gt 0 81 Ath A TED ee f O16 fh a ED II stresses 298 chips gt 0 739 2004 2009 Kazu Co pyrig ht amp 4 1 6 Format of the Correlation Data Please open the file Correlation_Ath_Gene_v csv with Microsoft Excel a a5 4 Data Analysis Advanced As the row number in the file exceeds the Excel s capacity the whole data could not be shown But anyway you can check the format of the file 1 AtleQi060 Atte 46830 0 855 AteN060 At3e09600 0813 Ate01060 Atte 39960 0 8 AteNO80 At3e48730 og AteQi080 At
22. appear under the pathway map in the main window By selecting the combination name and clicking the Select button the pathway map area will be redraw to the Multiple Map Mode and the combination of the maps will appear BO KaPPA View4 Manual for Beginners TCA cycle r 7 i Fhada prea e i amah eain a i E a E H a te ee sd m Siini om r herp ihm ibar s pa i oa Hina bree i E F mire pham C E mie pick LET FE ENE L kiami nap ia Aromatic amino acid biosynthesis wie Pantone phota pehey J 1 r Seip chee fn pe i ood i o in pices i m T Lj TE I g Sal pps oiha re rpi ie L Trimi ci Aberli geim tpi iain m smi pin T a C thee HEF Bungie hiir Ha ol H mipaineri inin Miia ampir er lids kanm m repai oh m ete n aa oie ri de co LS SS Tri Multiple Map Multiple Map 1 As described before the top left map of the Multiple Map is related to the pathway tree You can replace the top left map by selecting another map in the pathway tree To exit the Multiple Map mode select Single Map from the pull down list and click Select button Multiple Map L Single Map i Sos me Map 4 4 Utilization of User Maps GS _4 Data Analysis Advanced S Users can create their own pathway maps and utilize them in KaPPA View4 It would help you to analyze non metabolic genes which don t exist on the default maps to ma
23. ata Comments All values are set to 0 Data Experenent_ID KEPT 2 Nata Penecement Name Icamnie All eaves 21 davai zj COCCO mies Detailed information for the experiment set and each experiment is written in the fields start with Set_ and Data_ respectively Experiment Information Experiment Set Information Experiment Type TRANSCRIPT set_ Set ID KEST1 set_Experiment Set Name Ath Transcripts Demo Data set_Array Type AGI codes Set_Description Default data for demonstration set_Depositor Name sakural Expenments Data_Experiment_ID KEPT1_ 1 Data_Experiment_Name sample 0 All zero control Data_ Value Type quantitative Data_Comments All values are set to 0 The kinds of the fields were listed in the pull down in the search control panel Therefore you can optionally narrow down the search results by field specific key words ES KaPPA View4 Manual for Beginners Step 1 To show the data list select a species and experiment type and then press the Search button Species Arabidopsis thaliana Experiment Type f TRANSCRIPT METABOLITE Upload User optional All Upload Date optional E Experiment Set Header optional Depositor Name Experiment Data Header Description optional Experiment Set Name Experiments Reset Related Experiment Set ID Species This search option is useful for the
24. ccccecccccceeesseeeseeeeeeeesseseeseeeeeseeeeseaseeeeeeees 28 4 1 1 Viewing the Correlation Data ccccccccsseesecccceecceeeeeeeeeeeeeaeeeeeeeeessesaaaeeeeeeessseaaeeeeeeees 29 4 1 2 Filtering the Data to view Range of the Correlation Values cccccsseeeeeeeeeeeeeeeeeees 30 4 1 3 Filtering the Data to View Number of the Lines ccceccseeeceeeeeeeeeeeeeeeeeeeeeseeeeeeeeeas 31 4 1 3 Details of the Correlation Data Displayed cccccceececccceeeeeeeeeeeeeeeeesaeeeeeeeeeeesaaaeeees 32 4 1 4 Displaying densities of the Correlation Lines on the Bird s Eye map5 00cceeeee 33 C KaPPA View4 Manual for Beginners 4 1 5 Uploading Users Own Correlation Data ccccccccsseeeeeeeeeeeeeeeeeeeeeeessaaeeseeeeeeessaaaeeees 34 4 1 6 Format of the Correlation Data cccccccccccccssseeeccceeeceeeeeeeeeeeeeseeeeeeeeeeeeesaeeeeeseeeesssaaaaeees 35 4 2 ONMMNS MAD sscetcavacacetvegweencushesnacebie on niie e e ai a dodanie 36 4 3 Creation of Multiple Map cccccccssseccceccseseceecceeeseceescseeseeeeeesseaeeeessaaseeeesssaaeeeess 39 4 4 Utilization of User Maps ccccccccccsseeseeeeceeeeeeeeeeeeeeseeeesseeeseeeeessaeeeeeessaaeeeeessaaees 41 5 Other FPUNGHONS sosiaa a a EE Ea aai 45 5 1 Universal Map Mode css scsceassedsncctaerecesnadeadseveetenes vachexsatasencuansnects naeocapasoneenseueseste sos 45 5 2 Comparing two experiments in a SPECIES ccccccc
25. csv You can see two rows of header in both the microarray and the metabolite data files The first row starts with arrayexp or compexp In the uploading process the KaPPA View system recognizes the experiment type by this cell The subsequent columns of the first row are the data names The second row always starts with rep and the subsequent columns represent the repetition numbers Remember that the Sample Ath C and D of microarray data contained experimental duplication Therefore the repetition numbers of it were set to 1 and 2 see the second row of Column D and E in the figure 2 5 1 The experimental values see below of the repetitions within an experiment are averaged for each gene or metabolite and the representative values are utilized to display on the pathway maps The third and the subsequent rows describe the experimental data The first column is IDs for microarray probes microarray data or for compounds metabolite data and the second to the last columns are the experimental values T 2 Starting the Analysis The list of the valid probe IDs that KaPPA View can accept are written in the statistics page which is linked from the top page of the KaPPA View site KaPPA View 4 Kazusa Plant Pathway Viewer Home Overview News Statistics Download Link Publicd ay Login Welcome to KaPPA View4 Classi Go tc Nar Enter Pas Gene and Probe infromation Specnes G
26. d it can list up co expressing genes of Arabidopsis for a query gene of researcher s interest KaPPA View4 provides a function to overlay gene co expression data onto the pathway maps Data representation in this manner helps to grasp the gene to gene relationships on the aspect of metabolisms KaPPA View4 can represent metabolite to metabolite correlations too As an index of co expression between the genes correlation coefficients have been typically used Hence the functions of KaPPA View4 concerning to the co expression of the genes or co accumulation of the metabolites are referred like correlation functions However the data which KaPPA View4 accepts is not restricted in the correlations Any data which represents gene to gene or metabolite to metabolite relationships as numerical values can be utilized For example protein to protein interaction data described by 0 or 1 is zj n S KaPPA View4 Manual for Beginners acceptable Please try to project your own ideas onto the pathway maps with KaPPA View4 4 1 1 Viewing the Correlation Data The following control panel is displayed under the pathway maps Here the users can choose the correlation data to view Correlation Line Correlation Color Range Number Gene No Lines TRY foc ho High fo 70 Compound _ No Lines gt GREENS foc ho High fo 7o Update Correlation In the defaults several gene co expression data provided by ATTED II can be selected
27. d that the pathway was activated because expressions of a large proportion of the genes 1n the pathway were up When more than one Compared Experiment Pair have been set in the analysis a pull down list is displayed at the bottom left of the Bird s Eye map You can select the data to view here zt KaPPA View4 Manual for Beginners Compared Experiment Displaying Correlation Data In the case Correlation is selected for the display mode densities of the correlations on the maps are displayed in the bars Details are described later 4 1 Displaying the Correlation Data OT 4 Data Analysis Advanced 4 Data Analysis Advanced Various functions for analyzing omics data based on the pathway maps are implemented in KaPPA View4 Each of them is described in this chapter Combinations of the functions will provide new points of view for decoding omics data 4 1 Displaying the Correlation Data In the recent years a huge number of microarray data are available on public and it contributes to generate co expression data as a novel data resource A group of genes which are involved in a certain biological system could be expressed in coordinate manner throughout various conditions Therefore focusing on the unknown genes which co expressing with well known genes could give a hint to uncover the functions of the unknown genes ATTED II http atted jp for example is one of vanguards of such approaches an
28. displayed Please specify a species A following window will open Simple Map Create New Simple Map Created Maps Map Name Gene List Pe Add Clear 4 Load From File Load From Map Redraw Let s create a Simple Map from gene ID list in the sample data Push the Browse button and select a file named myb_agris txt in the simpleMap folder By clicking the Load From File button the gene IDs written in the file is read and displayed in the Gene List area 37 4 Data Analysis Advanced New Simple Map Map Name Gene List At3q27920 a At3g09230 At3q12820 At2q25230 At2g32460 At4g21440 At1g63910 At2g26950 Atig69560 At3q01140 cear You can input the gene IDs directly in the Gene List area By clicking the Load From Map the gene IDs on the pathway map currently viewed is displayed in the Gene List area Input Myb Family AGRIS as Map Name and press Add button New Simple Map Map Name Myb Family AGRIS Gene List Then the registered map name is appeared in the Created Maps area Created Maps Myb Family AGRIS Click the Redraw button to redraw the pathway tree in the main window Finally close the window The registered map is appeared under the new branch named Simple Map in the pathway tree You can use it for your analyses same as the default maps Ee KaPPA View4 Manual for Beginners Arabid
29. e Glyceraldehyde 3 phoephate phoephate jahydrogenase 20 m NADP phoephorylating ED BE Ribul e bisphosphate s carbo x ase small subunit F bisphosphate alddase Aldolase D Ribulose 1 5 bisphosphate D Xylulose m Phosphoribulokinase 5 phcephate D Fructose 1 6 bisphosphate D Ribulose 5 phoephate Fructoee bisphosphatase D Ribulose 5 phosphate S epimerase D Erythroes 4 phosphate Ah GOES 00080 BABA x x6 Fructoge bisphosphatase aldolase Glyceraldehyde 3 Alddase phcephate fo B E Ribose 5 phosphate isomerase Sedoheptulose Ribose 5 phosphate unico11 bisphosphatase ah BE Osa 2 20080315 ah E D Sedoheptulose 7 Osa D Sedoheptulose phcephate 1 7 bisphoephate Transketolase 5 Other Functions The Simple Maps and The User Maps which are postulated to belong to a specific species are not utilized in the Universal Map Mode Representation of correlation lines is not available too 5 2 Comparing two experiments in a species If there are several Compared Experiment Pairs for a species two of them can be represented simultaneously on a pathway map When several Compared Experiment Sets are set for one species a button titled Compare will be appeared Please check on two sets originated from one species and click the Compare button Ath Data3 Show All Experime e Then you get the comparati
30. e calculations By checking off the repetition ID in the Repetition column the data is omitted for further analysis Repetition M1 M2 In this tutorial it is not needed to change the settings Please push the Next button then the map browsing window will appear Plant metaboles pathways zj Map Vits fuming acid nucleic acid 4 Salaci gt PPP ei tha p Asiain liek ee ee Select a name of species or Unnvercal from the pull down list 2 Click on a map ora Map Category on the metabolic Paina Tree 3 1 1 Advanced Search Options When Set ID or Exp ID was clicked on the data list the details of the experiment set and each experiment data were shown in a pop up window aT 3 Data Analysis Basic SeeD Set Name Array Type Uploaded Date kesti 4th Transcripts AGI codes 3 2009 10 28 Demo Data a Tal KEPT1_1 sample _0 All 2 control All values are set to 0 quantitative Bal KEPT1 2 N iple _A1 Leaves 21 d fe tme Aprkanmscre hor evverinenttrevien eiecactertinetethits m same A2 TS cultured Experiment Information Expenment Set Information Expenment Type TRANSCRIPT Set_Set 10 KESTI Set_Expenment Set Name Alh Transcripts Demo Data Set_Array Type AGI codes Set Description Default data for demonstration Set_Depositar Name sakura Experiments Data_Experiment_ID KEPTI_1 Data_Experenent_Name sammple_0 All zero control Data_Value Type quantitative D
31. e limit value for the strongest color could be changed in the Histogram a a 3 Data Analysis Basic Element List Correlation List Histogram olor Legend Download Plain Map Print Map BE hh E E for kes km I fm br if Salle Ead ama ima a Waa tac a ot a Input the limit value 1 n the Highest Linear Value field By clicking the Cale button you can check the frequency distribution of the elements in each color Push the Submit button to fix the setting Please refer to the Advanced Manual for details 3 2 3 Switching the Compared Experiment Pair In the operation so far we selected two Compared Experiment Pairs namely Ath 1 and Ath 2 The data which you are currently browsing is checked in the upper control panel In the figure below the data from Ath 1 is represented Show All Experiments Ath 1 Transcript Sample Ath A Sample Ath B Metabolite Sample Ath A Sample Ath B Calvin cycle Phosphoglycerate kinase 3 Phoepho D glycerate f Oi Glycolate pathway Gluconeogenesis 3 Phoepho D glycaroyl mama ehate Glyceraldehyde hata Triceaphosphate isomerase Glyceraldehyde 3 phoephate dehydrogenase NADP phoephorylating Ribulcee bisphosphate H carboxylase small subunit Dihydroxyacetone pheephate i Transketolase Carbon dicxide Carbon diowd Atmosphere bisphosphate aldclase D
32. ed as ZIP decompress the file with proper application before use O data_metabolo me Odata transcriptome post simple Map S URL link user Map 2 Readme EM txt E Feadme_JdF txt The resulted folder contains several sub folders Please refer to the Readme _EN txt for their brief introductions 1 3 User Setup As KaPPA View4 is a web based system it works well with major web browsers Microsoft InternetExplorer Firefox Google Chrome Safari and Opera on any operating systems Windows XP Vista 7 Mac OS X and Linux Although the Adobe Flash Player plug in ver 9 or higher is required to display the pathway maps it 1s already installed in your browser in the most ay KaPPA View4 Manual for Beginners cases If your browser doesn t have it please install it according to the following site http www adobe com products flashplayer Please be sure to install the latest version of java plug in in your browser The older version might be cause of unexpected trouble in page constructions The operation of KaPPA View4 was tested in the following settings Windows XP Vista 7 Microsoft Mac OS X Apple Browser Internet Explorer 6 7 8 Safari 4 0 4 Mozilla Firefox 3 0 10 3 5 2 3 6 10 Mozilla Firefox 3 5 6 3 6 10 Google Chrome 3 0 6 0 Opera 9 63 10 10 In the case of Opera on Mac OS X the full screen view of the maps does not work Disable the pop up blocking function of your bro
33. ent Hame Daa Satc per Date Hiad r Experment Data Heade ee O an Chaar All Search Reset On the lower part of the window a list of data which are currently available will be displayed Showing 10 7 per page Showing 1 2 of 2 Set ID Set Name Array Type No of Exp Uploaded Date Related Data gt KESTI M NEE iiia 8 2009 10 28 Data gt TempSet_000001 TempSet_000001 AGI codes 4 2009 12 09 The data uploaded in the section 2 is registered under the Set Name Tempset_000001 A list of experiment data contained in the experiment set is shown by clicking the arrow head gt Peer Y TempSet_000001 TempSet_000001 AGI codes 5 2010 01 03 Exp ID Exp Name Comment Type Cd TempExp_000001 Sample Ath A quantitative Cd TempExp_000002 Sample Ath B quantitative Cd TempExp_000003 Sample Ath C quantitative Cd TempExp 000004 Sample Ath D quantitative Cd TempExp_000005 Sample All Zero Control quantitative Click the data icon E9 on the left of the experiment data Sample Ath A The name is appeared in the top right panel Selected Experiment Transcript Sample Ath A Metabolite Compared Experiment Name Set001 Add Clear All JA Oo 4 Then click on the data icon of Sample Ath B The experiment name is appeared as the second one wat KaPPA View4 Manual for Beginners Selected Experiment Transcript Sample Ath A Cd SampleAthB Metabolite Cd r C
34. ert ILD Probe 1 Sanap Array Type Abila Arabidopsis thaliana AGI codes trom TAIGH game as Gane O Atigiz345 AGI codes ath ces iiia RAP Ss Oighisrea2 Oryza sativa RAF DE build 5 locus si Phat a ah aa stat RAP DG transcripts It al ix Pics Ca 3 Eh I ID nar isice 1 1 51_6_at Oryza sativa RAP DB transcript RAP D8 build 5 transcripts Same as Gane Os0101a6100 01 RAPS transcript sal Solanum lyeopersicum Tomato AMymetix Tomato GeneChip proves Same as Genel Les 1020 2 41_at Afiymetrix Lotus Erpamenws p til ei he Karasa i I hi FTE mar Fi id i 1 Full lists of the probe IDs are also available from Download on the main menu appeared after logging in Select information as Data Type and find the Feature files The prefix of the file Ath_ Lja_ Osa_ and Sly_ stands for the species name as listed in the Statistics page For associating the gene expression values detected by probe on the microarray to the probe IDs on KaPPA View4 we prepared a Java tool KaPPA Average which is available from the following URL http kpv kazusa or jp kpv4 information tools_jp html On the preparation of metabolite data you have to know the compound IDs used in KaPPA View4 Please refer to a file named Uni_compoundInfo_yyyymmdd csv which is available from the Download menu or search the metabolite at Search on the main menu You have to input the experimental values as log scale for the probes negative to positive real values and as li
35. es the central function of KaPPA View4 e Map View You can browse plain pathway maps with no data from here e Search You can search genes metabolites and enzyme reactions from here and access to the pathway maps which they are on Homology search function by blast to find genes is also provided e Download The default experimental data publicly available on the KaPPA View4 and information data for genes metabolites reactions and maps for each species are downloadable as text files 2 3 Logoff You can logoff from the system by clicking Log off on top right of the main window Online Help amp Create Account Log off j If you don t do any operations for 60 min after you log in the system regards as you are log off You are automatically log off when you close all the o 7 2 Starting the Analysis browser s windows too All your data uploaded according to the next section are going to be deleted from the system after log off 2 4 Uploading Experimental Data 2 4 1 Uploading of DNA microarray data Press the Temporary Upload on the main menu Main Temporary Upload Analysi Map View Search Download The following window will be displayed Temporary Upload Experiment User Map Correlation Experiment File 8 Upload Click the Browse button and select a data file As an example select a file named Sample_Ath_gene_v csv in the data_transcriptome folder
36. es near by the Squares with gt By clicking the corresponding When there is not an enough space to enzyme reactions this symbol is displayed By clicking this the symbols of the genes are shown in a pop up window KaPPA View4 Manual for Beginners 3 2 2 Colors of the symbols The symbol colors correspond to the values of the elements Click on the Color Legend at the bottom of the window Element List Correlation List Histograny Color aon Download Plain Map Print Map Copynght 2004 2009 Kazusa DNA Research Institute All Rights Reserved Relationships between the colors and the ranges of the values of transcript and metabolite changes are displayed in a small window fo Wor PAS Views Color Legend Wind ep e Ty ay a iinder siioni nT Color L agend Transcript Metab msenpl Metabolite lofialRatio Ratio Lincar Scale Lower Lipper Color Lower Upper biarin G 100 0 1000000 rT EE ec aa 100 0 0 3 0 499 y id 26 853 0 1 0 1 a 0518 1 939 122 7 10x it it N In this example the gene symbols are drawn in red when the log10 ratio of them in the comparison of the experiments was greater than or equal to 0 699 5 fold change As shown here the up regulated genes and the increased metabolites are drawn in reddish color the down regulated genes and decreased metabolites are in greenish color and the genes and metabolites of no change are in yellow Th
37. eseeeeseeeeeeeeeaeeeeeeeeeeeessaaaaeeeeeeeeees 48 5 3 Utilization from the outside SYSTEMS ccccseeeeeceeceseeeeeeceeeeeeeeeseeeeeeeesseaeeeeeessaaess 48 Bo tlcs WG Harare cede eee sce nate secre cee eee geetecteee bce dae ances osen dol assisneenceeesancoameanenoneedosesaeeesee eeesceae 49 5 3 2 POST Data Transferring FUNCTION ccccceeeccccceeeceeeeeeeeeeeeeseeeeeeeeeeeeeseeeaeeeeeeeessaaaaeees 49 6 USer ACCOUNTS ices testers san ce seeps cane ccs etmeceanweteacceesadeweasscoeeassseacencenseateceneriaunes 52 6 1 Creating AN ACCOUNL ccccccccccsssseecececeseecececaeaeecececeaueeeeecessaueeesssaaseeeeessaaeeeeeeesaas 52 6 2 Expiration of the Power USE ccccceccccecceseeeeeecaeeeeeeeseaeeeseeeessesseeeessaaeeeeeessaaess 53 Bod OWEN User OCI Vas cteccs costegessacccececentmestsaescecenseneceesarsenectss saved sneeeusasacseeeeeasdsepeimeseseceas 53 6 4 Power User s M nu ccccccccccssssececeeceeeeceeeceeaeceeeseeaeeeeeeesegeeeessaeaeeeeessageeeeseesaas 54 ZMS and TIDS sees canceeecrece ves e E A ENEE E ATG RNE 55 7 1 Representation of non omics data on the maps sssssssessssssssssssrrrrresssrnnrrrreese 55 MONY aea EE E E 57 9 Eding HISTONE S see scten cece een scesbaceneeccteccetenecanwanenessedeuseaeusacaecaeseceaseiceiecseraeens 58 Table of Contents KaPPA View4 Manual for Beginners 1 Introduction KaPPA View4 http kpv kazusa or jp kpv4 is a metabolic pathway database which i
38. heS5220 0 593 6 4te01080 At3g29185 0 891 7 4te01080 At4e 29060 0 89 8 ate01080 Atig32990 0 588 PS Atle01080 At1g05190 0 886 tie0iog0 Atle 79850 0 582 AteNO80 At2e37660 0 881 Ate0i080 Atles4510 0 58 AteNO80 Athel 3610 0 88 tie0iog0 Athed7190 0 877 1R A amp H aM AAN AiR For In the case of gene correlation data a row consists of three columns 1 e gene ID gene ID and value correlation coefficient In the case of metabolite correlation a row contains compound ID compound ID and value correlation coefficient The data file must be saved in a comma separated vector CSV format 4 2 Simple Map As KaPPA View represents the gene expression data in the symbols on the pathway maps the genes not drawn on the maps cannot be analyzed While the microarray data and co expression data include a lot of non metabolic genes and unknown genes To expand the target genes for the analysis KaPPA View4 serves a function creating a Simple Map according to the gene ID list users input Square symbols for the genes in the ID list are arrayed on the simple map Myb Family AGRIS BHRER BBB RB EBEBBBRBORBBOORBERBBBBRBBBORBORBHBRORBBERREEEE ES BOE TETEE E ERB EBRBHBHBORORERBEBE E OBE BBR HRBEBHROBDOOAEB BHROBBRROBE BREE BRR ETRE E BER BOOB RBBB BERRBHRERBRHRBEOBOBDA BHROBEB BEE RBSBHRBEAEBBE B Ea KaPPA View4 Manual for Beginners A full list of gene IDs used in the KaPPA View system is available from the Download
39. iew4 Manual for Beginners Example of POST transtered Map Giycerol metabolism Kode Caio Sorete Map Oo Tar oO hk Add Rlated Map Me Lares REEN ps fio TEE Upang Gonpa gn User Map data could be included in the POST data too After jumping to the KaPPA View4 users can continue to browse the data and start next analysis with the posted data Details on the transferring procedure sample code of PHP and the format of the data file are described in the Advanced Manual 6 User Accounts 6 User Accounts After logging in to the KaPPA View4 system as a common user Guest User you can create freely your own account with a simple procedure Power User If you get your account you can save your own experiment data correlation data and User Map data on KaPPA View4 It helps you to start the analyses immediately after logging in There are no differences on the analysis functions between the user authorities 6 1 Creating an Account Log in as guest KaPPA View 4 Kazusa Plant Pathway Viewer Login Enter with your name and password Enter as a guest Name Guest Login Password in Click Create Account on the top right of the browser window Online Help G Create Account amp Log off GUEST Temporary Upload Analysis Map View Search Download A pop up window will open Enter your account name and e mail address and then press the Submit button s2 a
40. ism N rr ns rt tt L Isoleucine Uniooo0s 2008 03 28 L Leucine The experiment values are represented in this figure as colors of the symbols The correlation lines can be represented too when users are browsing the plain maps without experimental data 4 1 2 Filtering the Data to view Range of the Correlation Values The correlation data currently selected was calculated from 1388 Arabidopsis GeneChips Affymetrix and the gene to gene relationships which showed more than or equal to 0 6 of Pearson s Correlation Coefficients were included When the users would like to focus on much stronger relationships they can filter the data by the correlation values Please enter 0 9 in the left hand field of the Range column Click the Update Correlation button BO KaPPA View4 Manual for Beginners Number High j0 729 0 76 Then only the lines having values between 0 9 and 1 0 are displayed Leucine valine isoleucine and alanine biosynthesis Lysine threonine anc f N Glycolysis methionine biosynthesis Ketol acid reductoisomerase Acatolactate synthase Traa ele H 2 Oxobutancate wo 2 3 Dihydroxy isovalerate m Doo L Threonine 2 Acatolactate Dihydroxyacd Acato 5 s dehydratase cetoladate synthase Branched chain amino acid aminotransferase n Alani aminotransferase 2 Aceto 2 hydroxybutyrate 2 Ketoisovalerate o Fa Ketol acid reductoisomera
41. ke more beautiful pathway representations to analyze with the maps with careful curation of the gene assignments and so on The user created maps User Maps have to be prepared in Scalable Vector Graphics SVG format We recommend doing it with a freeware Inkscape Please refer to the Manual of User Map Creation for the details User defined gene IDs and compound IDs could be included in the User Map data If the IDs and their values are written in the analyzing data the symbols of the user defined elements are painted with color like as the pre drawn ones on the default maps Let s look at the way to upload and utilize the User Maps here with a sample SVG file Click Temporary Upload on the Main Menu and select the User Map tab User Map File a Upload Click the Browse button and select a file named UserMap_GS GOGAT_v svg in the userMap folder in the sample data Press the Upload button then a preview will appear KaPPA View4 Manual for Beginners Temporary Upload Experiment User Map Correlation User Map File AR Upload Map Preview The GS GOGAT Cycle Amino acids Nucleotides Chlorophyll A etc Glutamate synthase CO NADK type 8 0 Le one HO N OH NH O L Giutamate Nitrate reductase NO3 TCA Cycle Map Name Comment submit Input a map name in the Map Name field here input User Map 1 then click the Submit butto
42. n The uploading will successfully finish with the following message The operation succeeded The uploaded User Map will appear in the pathway tree under the branch name User Map You can utilize it same as the default maps in your analyses 4 Data Analysis Advanced Arabidopsis thaliana x User Map 1 Arabidopsis thaliana metab El Compared Experiments Carbohydrate metabolisr Amino acid nucleic acid ed ne ipids metabolism soprenoid metabolism Ath 1 Phenylpropanoid and shi Transcript Sample Ath A Sample Ath B Tenn teins and mined Metabolite Sample Ath A Sample Ath B E Myb Family AGRIS q A Glutamine synthetase Create Simple Map m Ammonia Nitrite reductase a NO2 Nitrite Nitrate reductase NO3 Nitrate 44 Show All Experiments The GS GOGAT Cycle Amino acids Nucleotides Chlorophyll etc Glutamate synthase E sONADH type o o ae a A RA HO OH 2 Oxoglutarate TCA Cycle TCA Cycle KaPPA View4 Manual for Beginners 5 Other Functions In this chapter we briefly introduce other functions of KaPPA View4 Please refer to the Advanced Manual for the details of each 5 1 Universal Map Mode There is an item named Universal in the pull down list for species selection Arabidopsis thaliana Universal Arabidopsis thaliana Lotus japonicus Oryza sativa Solanum lycopersicum
43. n ai aa aca ate Ae z 1 nae pape aaa ace main wear hm Low Small On the Bird s Eye View Maps you can view the summarized values for all maps and find out the pathways which have changed considerably Arabidopsis thaliana melabolic pathways SOE aa aemm 2 os bes 1 3 m ad oe e e Se 5 AEP Papa a oa Ss a E id ee re EZ z a PS ioe a E Ea e nea EON EE G A rr ee E ea a E rma a J Ll oa avr my SST a i ee o i EZA i joe oo e a O HTA a TO e ure a gt l Bea o ae r Ae a u Peien mm eo a EEE iru m E Or 1 beare t maru k lt pee Pe C TE eee mirem eee dn M aT e nka e EE iee i me SSS i _ E re eem arp hao i a m T EEE e oo e Aas O e fom Cr i e _ Mam 3 a Aro t b lt ss lt lt fe a m E Cs an B o CE E a SS E TES Non metabolic genes which do not exist on the maps such as transcription factors can be analyzed By entering the gene IDs you can create simplified maps timia Map Crear Hew Sirraple Map Map H rri Myt Family AGRIS Myb Family AGRIS Gene List BOBOODOBOODOBRBOORBBOADBOBAODOOOBOOOOOOCOOG08OOG QDHOHOOBODOOBDOBBOOARABRABODOOOABAOBOARBOOOOOGBOKOO0O8ED BOBOOBBOOOODOOSBSDRRABDRBBBOBOOBBOBBBBOOOADDA BOOGOOBOOO0OGBOBOEBBHEOOD In addition the users can also use the pathway
44. near scale for the metabolites positive real values except zero Save the data files as text files formatted in comma separated vector CSV ETS M KaPPA View4 Manual for Beginners 3 Data Analysis Basic Let s move on to data analyses on the pathway maps In this section we first show the procedure how to select the data from the uploaded data set and then explain basic functions for data browsing 3 1 Data selection for browsing In KaPPA View4 a unit of analyzing data is defined as a compared data between two experiments We refer this unit a Compared Experiment One Compared Experiment is comprised of a pair of gene expression data a pair of metabolite data or both of them Compared Experiment Gene expression data Exp Data 1 Metabolite data Exp Data 1 Let s try to make a Compared Experiment using the data uploaded in the section 2 Click Analysis on the main menu Main Temporary Upload Analysis Map View search Download A data search window will appear Please check that Arabidopsis thaliana is selected as Species and TRANSCRIPT for Experiment Type Then press the Search button Tn 3 Data Analysis Basic Species Arabidopsis tholana Selected Experiment ratecrpl Expenment Type TRANSCRIPT METABOLITE EF r Upload User All La Mstabelae Upload Date z E F d za E Expenmant Set Header z AND COR Compared Expenm
45. no di and oligos kinase 3 Phoepho i IP olysaccharide metal Gluconeogenesis 3 Phoepho D glyceroyl D glycerate Glycolate pathway omo phcephate Glyceraldehyde Miscellaneous carboh Triceephosphate isomerase o 3 phosphate Amino acid nucleic acid m m Dihydroxyacetone Glyceraldehyde 3 phoephate phcephate dehydrogenase NADP phoephorylating Ribulcee bisphosphate mI carboxylase small subunit Kjo gt Create Simple Map bisphosphate aldolase Aldolase Carbon dicxide Carbon dioxide T2nsketolase D Ribulose Atmosphere 1 5 bisphosphate D Fructose 6 phoephate Phosphoribulckinage D Xylulose 5 phoephate D Fructoge 1 6 bisphosphate D Ribulose 5 Fructoee bisphosphatase D Ribulose 5 phosphate S apimerase D Erythroee 4 phosphate As shown here you can browse the transcriptome and metabolome data by selecting the species and the pathway maps 3 2 1 Symbols on the pathway maps The elements such as genes and metabolites on the pathway maps are represented as symbols below Element Squares m etabolites Circles enzyme arrows The color of the arrows correspond to reactions the mean value of the genes assigned to the reactions links to the pathway name other maps pathway maps is displayed round rectangles with a text oo draw all the gen
46. oarray data described as the transcript IDs can be analyzed with it The data also can be analyzed in the updated Oryza sativa by selecting the array type RAP DB transcript A main window for Power Users will be displayed ns 5 6 User Accounts KaPPA View 4 me 9 2 Pe Main Temporary Ugioad Analysis Map View Search Download Mair The Side Menu for Power Users Tt iata i ased t h the T S a until your Menu Bar Tempolary Upload 6 4 Power User s Menu There is a Power User s Menu Side Menu on the main page Personal gt 5 Ea gt Experiment Upload User Map Upload Correlation Upload Personal Data List Utilities gt ri Password Change Profile Edit Personal Block Here Power Users can upload their own experiment data User Map data and correlation data The uploaded data will be stored in the KaPPA View server and kept until the expiration of the account The data is strictly administrated in the system and is never seen by the other users Management of the data 1 e deletion and edition is available in the Personal Data List Utilities Block Password changing and editing of user information is available here S E KaPPA View4 Manual for Beginners 7 Hints and Tips In this section we will introduce some advanced usage of the KaPPA View4 7 1 Representation of non omics data on the maps In usual the function for the experimental data u
47. ompared Experiment Name Set001 Add Clear Al Let s try to select metabolite data In this state please check on METABOLITE for experiment type and press Search button gecscseg iY TempSet_000002 TempSet_000002 4 2010 01 03 Exp ID Exp Name Comment Type Cd TempExp_ 000001 Sample Ath A quantitative CG TempExp_ 000002 Sample Ath B quantitative E TempExp_000003 Sample Ath C quantitative IP TempExp_000004 Sample All 1 Control quantitative The second data temporary uploaded is registered under the Set Name TempSet_000002 Expand the list by clicking arrow head gt and select experiments Sample Ath A and Sample Ath B The top right panel will be like this Selected Experiment Transcript Sample Ath A Cd Sample Ath B Cd Metabolite Sample Ath A Cd Sample Ath B Cd Compared Experiment Name Set001 Add Clear Al Let s register this combination of experiment data as a Compared Experiment Please type Ath 1 in the Compared Experiment Name field and press Add button At the bottom of the top right panel the Compared Experiment Name will appear Compared Experiment List W Ath1 a a Next gt gt ns a 3 Data Analysis Basic You can register more than one Compared Experiments Try to register next One Select TRANSCRIPT for experiment type press Search button to show the data list select the experiment data Sample Ath C and Sample Ath D and register this
48. onsesenssoneesneesons 13 3 1 Data Selection for DrOWSING ccccccscccccsssseecceseeecsaeeecseseeeseaseeeessasessagseeessgeeeses 13 3 1 1 Advanced Search Options ccccccccececcccceeceeeeseeceeeeeceeeeeeeeeeeeessaesseeeeeeessseeaeeeeeeessaaaaeees 17 3 2 Data browsing ON the MANS cccccseeececseeeeeeeeeeeeeeseeeeeeseaseeeseaeeeeesageeesaseeenseeeeeeas 19 3 2 1 Symbols on the pathway MANS ccccccecsseseceeeeeeeeeeeeeeeeeceeeeeeeeeeeeseeeeeesseeeeeeeesseneeeeeeas 20 3 2 2 Colors Of the SYMDOIS srein enai E EENE EEEE AKiN 21 3 2 3 Switching the Compared Experiment Pair cccccccsceecccceeeseeeseeeeeeeesaeeeeeeeeeeessseeaeees 22 3 2 4 Details of genes metabolites and enzyme reactions cccccceeecceceeeeeeeeeeeeeeeeeeeeaaeees 23 3 3 The Bird s Eye Map sisveicnwisswnsvangensvexaasibbsiluaetalduriuaivesniamiehbavessuietnadsubivwisaversaemiebturrentins 24 Displaying the Map Names ccccccseecceseeeeeceeeeeceeeeeeeeeeeseeeeeesaaeeeeeeeeeessaeeesseeeeessaseeeneneeeens 25 Displaying the Experiment Data cccccsecccceseeeeceeseeceeeeeeceaeeecseseeceeueeessuseeesaueeesseseeesenseeess 25 Displaying Correlation DAN iiccsaccesnseiscemectetlecncaicteewshae vasacastideceras Veil bosuicds Meecha uedacestidcansatetsecoadeveets 27 4 Data Analysis AdVancCedd cccsscesscsseeceseceneeenseceeesenseeenssonseoesseeneeoeneneaes 28 4 1 Displaying the Correlation Data cccccc
49. opsis thaliana myb Family AGRIS Arabidopsis thaliana metab Compared Experiments ICarbohydrate metabolisr H Amino acid nucleic acid eri ea ipids metabolism Show All Experiments 2lsoprenoid metabolism Ath 1 Phenylpropanoid and shi Transcript Sample Ath A Sample Ath B a a er niia Metabolite Sample Ath A Sample Ath B Functional categories Simple Map Myb Family AGRIS E Mvb FamilwIAGRIS Enee EEN EEEE fii ining EEE E ninini iinne oe Boe Eng SEEE E EEE A Eirini EngnE E E nn AE E fiie e Eig Ering eee EE E A EEE E Bee Belen fol of 8 fon fon 0 E Ening cE Engg BBE fmi iniii a all Fa Create Simple Map 4 3 Creation of Multiple Map In KaPPA View4 at the maximum of 4 maps are simultaneously displayed on a single browser window This mode of view is called Multiple Map Mode which would help you to overview transcriptome and or metabolome changes in related metabolic pathways The user created Simple Maps 4 2 and the User Maps described later can be included in the Multiple Maps too Moreover the correlation lines see 4 1 are drawn across the each metabolic map Therefore the Multiple Map Mode provides an important basis for exploring regulatory mechanisms between genes and the metabolic pathways such as relationships between a transcription factor gene and metabolic pathways governed by the gene At the bottom of the pathway map you can see a button named Add Related Map Click the
50. ploading is used to upload omics data such as gene expressions transcriptome data and metabolite accumulations metabolome data Utilizing the function we can visualize the other data on the pathway maps as follows 1 Significances of the data detections on the microarrays ex P value log ratio from the Agilent s microarray 2 Probabilities of the data changes ex The results of t test 3 Existence of the genes or compounds ex Gene lists extracted from the microarray analysis A compound list of a standard chemical library Gene list for each GO evidence codes to check the reliability of gene annotations To prepare a data file as the same format to the experimental data files we can upload the data and represent on the pathway maps on KaPPA View4 In the case of 1 and 2 the significance and probability values are described in the data file instead of the detection values Of course the values should be scaled to fit to the color gradation of KaPPA View4 In the case of 3 existence of the genes or compounds should be described as a proper value ex 1 exists and 0 or null not exists for genes By setting proper values for multiple categories of the genes or compounds users can represent up to 9 categories in different colors simultaneously on the maps The functions for switching several experimental data to browse and for representing two experiments data simultaneously on a single map enable T Hint
51. s Eye map the names of the pathways are displayed in the bars You can change the contents in the bars by choosing the items from the Display Mode Display Mode Name Expernment Correlation Displaying the Map Names When the Name is selected for Display Mode the names of the pathway maps are displayed in the bars C02 fixation and cantral carbohydrate metabolism I flansdertbe rurda Displaying the Experiment Data o Ta 3 Data Analysis Basic When you select Experiment the bars turn to as below 202 fixation and cantral carbohydrate metabolism T 251 25 1 7172 a T3535 Dy M1515 Sn T T 3131 DM 187 T4606 Mt EE T7573 M oo T 4142 ha 11 11 T 1519 En 1 60 A The color gradation represents followings Ex 7 4203 EO E ooo T Transcripts The denominator shows the number of the genes drawn on the pathway map 43 genes The numerator indicates the number of the genes having valid values in the current data 42 genes values for one gene was invalid M Metabolites The valid metabolite number numerator 8 and the metabolites drawn on the map denominator 14 The numerator and denominator values at the pathway categories are the compiled values of all the pathways included in the category Color gradation of the bar The proportion of the genes or metabolites painted in the color Therefore if the bar for transcript was strongly painted in red it implie
52. s aimed to better understand metabolic regulation and to generate hypotheses from huge public available omics data 1 e transcriptome metabolome and co expressions of the genes This manual guides major functions of KaPPA View4 to facilitate the beginner users to understand how to use the system 1 1 Overview of KaPPA View4 When you upload your own DNA microarray data and or metabolite data to the system through the web browser KaPPA View4 displays the fitting of data for each gene or compound on the metabolic pathway maps By default approx 150 maps are available corresponding to Arabidopsis rice Lotus japonicus and tomato Upload KaPPA View 4 Kazusa Plant Pathway Viewer Display on the browser 7 Y KaPPA View4 eee 6 Server On the pathway maps genes and compounds are represented by squares and circles respectively The symbols are painted in different colors depending on the values such as changes in the ratio between two experiments and the amounts detected in one experiment ee Ge 1 Introduction Aromatic amine acid biosynthesis ia Ratio Expression aed Fenosa phoschate pactreny f Sis aa Pirar Exp A Exp B Accumulation herer hi oye a Prepares ienige Py oe amount veetee E E Color T moann aye heplerae ailai High Large aa He M fees Gmiaan saba asst Tre a a a ee No change m0 BLO r Oee Se Anan oyrini f E Faa
53. s and Tips users to browse the real experimental data and correlation data while checking the values of user s interest KaPPA View4 Manual for Beginners 8 Inquiry Please inform us all of your questions and requests about KaPPA View4 if there are by e mail e mail kappa view at kazusa or jp please replace at to O Editing history 9 Editing Histories ver 1 2 October 3 2010 Some figures were updated 1 3 User Settings was updated Details of the operations were added to 5 1 Universal Map Mode and 5 2 Comparing two experiments in a species 8 1 1 Advanced Search Options was added 6 Hints and Tips was added ver 1 1 July 1st 2010 The first release ssf
54. se synthase 2 3 Dihydroxy 3 methylvalerate 3 lsopropyimalate Dihydroxyacid dehydratase dehydratase 3 Isopropyimalatp dehydrogenase 2 Kato 3 methylvalerate S carboxy isecaproate i Branched chain aminc n d Branchec chain amino acid aminotransferase acid aminotransferase Leucine Valine and isoleucine metabolism Se gt 0 A lt r rs L lsoleucine Uni00008 2008 03 28 L Laucne 4 1 3 Filtering the Data to View Number of the Lines When the ranges are changed by the way described above a text like 3 is displayed in the Number column It was 29 before the filtering Number E hi High The value after the slash means the total number of the correlation lines currently represented on the maps The redundant relationships of the same combination of the genes are excluded from the count As there are in the case that the same gene is drawn at multiple places on a map the indicated number could be different from the line numbers drawn on the maps Correlations calculated in an element self correlations are excluded from the count even if they are included in the uploaded files ns eh 4 Data Analysis Advanced Anyway please enter 1 in the field written as 0 see below and click Update Correlation button Number High High 10 6 6 Then only the highest correlations is drawn like the following figure Leucine valine isoleucine and
55. setting as Compared Experiment named Ath 2 Selected Experiment Transcript Sample Ath C Cd Sample Ath D Cd Metabolite Add Clear Al As described here you can register a Compared Experiment Pair which has only microarray data Please push Next button to go to the next window Compared Experiment List M Ath1 A M Ath2 lA E In the window you can choose which experiment in the pair is the denominator for the ratio calculation Analysis Compare Exp Name Exp Name Data Type Species Repetition Ath 1 Sample Ath A Transcript Arabidopsis thaliana 4 Sample Ath B Transcript Arabidopsis thaliana 4 Sample Ath A Sample Ath B Compare Exp Name Exp Name Data Type Species Repetition Ath 1 Sample Ath A Metabolite Arabidopsis thaliana 4 Sample Ath B Metabolite Arabidopsis thaliana 1 M2 Sample Ath A Sample Ath B x Compare Exp Name Exp Name Data Type Species Repetition Ath 2 Sample Ath C Transcript Arabidopsis thaliana 1 M2 Sample Ath D Transcript Arabidopsis thaliana 4 2 Sample Ath C Sample Ath D x Please choose one of two from the pull down lists tel KaPPA View4 Manual for Beginners Compare Exp Name Exp Name Ath 1 Sample Ath A Sample Ath B Sample Ath A Sample Ath B Sample Ath A Sample Ath B Sample Ath B Sample Ath A K When the experimental repetition was included in the data you can select here which repetition data should be taken account of the averag
56. tabolites O are all painted in white The detailed sample information is represented above the pathway As exemplified here several Compared Experiment Pairs can be set in a single analysis and users can browse each of them by switchine the data It is suitable for browsing related data sets such as time course experiments 3 2 4 Details of genes metabolites and enzyme reactions You can get the detailed information about the symbols for genes metabolites and so on and enzyme reactions by clicking them on the pathway maps A window will open and you can see descriptions of the element values of the experiments 3 Data Analysis Basic Gene Information At3g12780 Gene ID 14 TAIR Annotation 1 AT3G12780 1 PGK1 PHOSPHOGLYCERATE KINASE 1 phosphoglycerate kinase 1 AT3G12780 1 similar to PGK PHOSPHOGLYCERATE KINASE Arabidopsis thaliana TAIR AT1G79550 2 similar to phosphoglycerate kinase putative Arabidopsis thaliana TAIR AT1G56190 1 similar to chloroplast phosphoglycerate kinase Populus nigra GB BAA33803 1 Description similar to Phosphoglycerate kinase Medicago truncatula GB ABE80998 1 similar to Phosphoglycerate kinase chloroplast precursor GB P50318 contains InterPro domain Phosphoglycerate kinase InterPro IPR001576 Currator summary nuclear phosphoglycerate kinase PGK1 Arabidopsis thaliana Map 1 Calvin cycle 2 Glycolysis gluconeogenesis 1 ROO11107 Sa 2 ROO11
57. ve visualization of two data 1 Set001 Transcript Ath A Ath B Metabolite Ath A Ath B 2 Set002 Transcript dark grown T678233 Metabolite Ath A comp test1 i Calvin cycle Phosphoglycerate Gluconeogenesis kinase j SPhospho C p 3 Phospho D alyceroy D glycerate phosphate BESS i Glycolate pathway e Glyceraldehyde A oo eo isomerase 3 phosphate D i DE 1 1D OO BO Ribulose bisphosphate ae Dihydroxyacetone phosphate carboxylase small subunit GB 7 DB i Transketolase D Ribulose bisphosphate Carbon dioxide Carbon dioxide aldolase Atmospher 1 5 bisphosphate Aldolase phosphate Phosphoribulokinase N D Fructose 1 6 5 phosphate VY bisphosphate Gi Em 2 Ge Fructose bisphosphatase D Ribulose 5 phosphate J p 5 e Mm D Ribulose 5 phosphate 3 epimerase w D Erythrose 4 phosphate Ribose 5 phosphate isomerase SEES OB8BO 2 See OOOO Fructose bisphosphatase aldolase Glyceraldehyde 3 phosphate Aldolase 5 3 Utilization from the outside systems eE T KaPPA View4 Manual for Beginners KaPPA View4 serves public interfaces to utilize the system from the outside servers and application programs 5 3 1 URL link By describing URLs in the following formats developers can make links
58. wser It is enabled in default for Safari Opera and recent Firefox and Google Chrome 1 4 Other Manuals A full guide of all operations of KaPPA View4 is written in Advanced Manual The procedure to create User Maps using free software Inkscape is described in detail in Manual of User Map Creation These manuals are also available form the top page of the KaPPA View4 site The Advanced Manual and the Manual of User Map Creation are under preparation They will be available in 2010 2 Starting the Analysis 2 Starting the Analysis Login and Upload of Experimental Data For the first step of the analyses we introduce the way to login main menu and how to upload the experimental data to KaPPA View4 2 1 Login Visit to the following URL and press Guest Login http 7 kpv kazisa or i16 kpv4 Login Welcome to KaPPA Views Classic Go to My Page Num Enter Password Piense cick Te tuflon to stan All Mhe data is Meaty acces sitie for gubsc loa n e users More advanced pou can save your own Gata on KaPPA Views Dy Creating your accourt Enter and cack Create Account for an rme aate regetabon tee Gene information for Oryza sata was changed August 15 2010 The transcnpe Os from RAP OS have been used for gene IDs of Oryza satma We changed the gene Os of t to the locus IDs from RAP OB s that the comelation data of nce could be represented The old settings are selecting the array type TRAP
59. y on KaPPA View4 a 5 Other Functions You can find an example of the POST function in the post folder of the sample data In this sample transfer of a formatted data file is performed by post method of HTML FORM Open the file ExamplePostForm_v html with your Internet Browser D imernis arr a8 erile and Selleme eakure ec WS A C Documents and Settrastsakurat 7 Oho 7 Ysa An example of POST data transfering function Select a file saved in the format for the KaPPA Viered POST data If it is accepted an URL will be displayed on the browser Accessing to the URL you can see the results on KaPPA Views4 pe DITUA KaPPA View4 YH 3 RIO z Select a sample file Sample_postData txt by the Browse button and then click the Submit button If KaPPA View4 successfully accept the request an URL will be returned In the HTML sample the URL is displayed on the browser window PE hipik pr kaucan heel upload action Werderre kilernal Explore j al mak G je hiper hpr karuan or jpkpyd upland act tt N Bile w i E bps kp kannar pinged up ed action ft A SEMANSLE ieee ee 4 100 Cut and paste the URL in the address field and jump to the site JS v J http kpv kazusa or jp kpv4 redirectaction lid ab14740e 4b15 434a 8b02 4d8fb16b6f9d referId e4a3985b 25ad 48b7 9fcc caa9elf4d e The result will be displayed on the browser window BO KaPPA V

Manual for beginners (pdf: 2.73 MB)

Contents

Download Pdf Manuals

Related Search

Related Contents