MetDisease user manual
Contents
1. MetDisease User Manual An App for Cytoscape Department of Computational Medicine amp Bioinformatics University of Michigan 3 1 2014 2014 University of Michigan Contents OG re tes ceca Paice ht ce sera eres erste create peed tc sete dtc ton te ieee daar E seu dato seuaew E sca necies eeauedisaceetareses 2 PD AU SOC e tae see se esc cw artes E eee a aneeonensmecocea noe E me eosuciagnetavarecteenteestewste 2 Workflow 1 Running MetDisease with a User Imported Metabolic Network cccccsseecceesseceeeeneeeeeeees 2 PANDE D Sa ee E teva ioas cee cian weap asa cence E 2 Workflow 2 Running MetDisease with a Network Created Using the MetScape App ccccccseseceeeeeeees 3 Eae Bb 6c ene ee eee rene A eee eee ee 3 Openine MeD SAS yo as ncaca cocneuensnertnvectueeietseuncnmnaernenenareeniues bent eaneunnaanniacnianeinnadramieaneu assed eendntommeny 4 MoR TIG lt r rere re me ee ee eee eee ee ee eee eee 5 Accessing Literature on Specific Metabolites and Diseases cccccccccseccceeececenececenseeeeeseseueceseueceeeeeenenses 6 Accessing Related MeSH Veli sisacatseisdetccntnacsesnistecenitcsenvandecatsaniesesanonscicauiscssatiwdedadenoaanasoed TENENS ENTEN 7 EO NE ATE E E E A E E EE E EER 9 PRE TNC OS E A E A 10 Please note that due to continuous software upgrades the images in this handout may not exactly mimic what you see on the screen Page 1 of 10 Overview MetDisease is an app for Cytoscape the bioinfo2. modes Urogenital Neoplasms 3 nodes Genital Neoplasms Male 3 nodes Penile Neoplasms 2 nodes Prostatic Neoplasms 1 node Accessing Literature on Specific Metabolites and Diseases 1 Click on a term in the MeSH term tree to highlight its mapped compound s in the drawn network Sarcosing dehydroge we 30036 S z Glycine N Table Panel J Hide Unmatched Terms Find MeSH Terms Eye Diseases 6 nodes B Male Urogenital Diseases 12 nodes E Genital Diseases Male 4 nodes Urogenital Abnormalities 2 nod Urogenital Neoplasms 3 nodes Genital Neoplasms Male 3 nodes Penile Neoplasms 2 nodes Zn Prostatic Neoplasms 1 node Urologic Neoplasms 2 nodes Page 6 of 10 2 Right Click on a compound in the network 3 Select MetDisease gt PubMed Citations e Edit Select 20061 Nested Networks P sferasi pps MetDisease gt PubMed Citations MetScape Related MeSH Terms External Links 9 gt Preferences gt Group 4 PubMed opens in a new browser window containing articles related to the designated compound and disease MeSH term PublMed gov US Natonal Library of Medicine Natonal Institutes of Health PubMed iai 22013201 22009695 21771248 21755295 21626193 21553390 21491110 21321584 212 EJ RSS Save search Advanced Show additional filters Display Settings v Summar
3. al Neoplasms Male 3 nodes Penile Neoplasms 2 nodes Prostatic Neoplasms 1 node Urologic Neoplasms 2 nodes 5 Right Click on a compound in the network 6 Select MetDisease gt Related MeSH Terms UUVJU Edit Select we Group Nested Networks MetScape External Links Preferences A rnksmATAeaaninaAtaA 7 Metab2MeSH Sartor et al 2012 opens in a new browser window showing other MeSH terms that are closely associated with the compound of interest Metab2MeSH annotates compounds with the concepts defined in MeSH The compound MeSH terms displayed are those that are significantly associated in PubMed abstracts and are ordered highest to lowest by significance score Users can filter by Diseases as a top level MeSH heading producing results similar to MetDisease Page 8 of 10 Search Metab2MeSH tema tie era N Compound search examples Sarcosine mathyimalonic acid uco se b phosphite MeSH term search exam Search by MeSH term Compound giabetes met ius metaociisim noon errors 206 MeSH descriptors and compounds found matching Sarcosine 0 requery Metab2MeSH with compound or MeSH descriptor Disclaimer Compound name matched Compound ID from PubChem at than Filter by top level MeSH Heading Show All Compound Compound HeSH Headings MeSH Descriptor MeSH Qualifier PubMed ID s Articles lgarcosing s 1088 Chemicals and Drug
4. ape Table Panel 2 Some MeSH terms are in bold while others are not a MeSH terms that are in bold have mapped compounds in the active network b MeSH terms that are not in bold have no matches in the active network Hamartoma no matches Neoplasms by Histologic Type 10 m Neoplasms by Site 9 nodes Neoplasms Experimental 7 nodes co Neoplasms Hormone Dependent no matches ag Neoplasms Multiple Primary 1 node Neoplasms Post Traumatic no matches 4 Neoplasms Radiation Induced 1 node 4 Neoplasms Second Primary no matches 3 To hide MeSH terms with no matches click the box next to Hide Unmatched Terms located above the MeSH tree Note the unmatched MeSH terms can be made visible again at any time by unchecking the box next to Hide Unmatched MeSH Terms Page 5 of 10 Table Panel Parasitic Diseases 6 noc _ Neoplasms 13 nodes Cysts 2 nodes Neoplasms by Histologic Type 10 noc Neoplasms by Site 9 nodes Neoplasms Experimental 7 nodes Neoplasms Multiple Primary 1 node O 8 8 8 8 4 Only those MeSH terms that have mapped compounds in the active network are now visible 5 Click the lsign next to any parent term to display its child term s If a term has a sign next to it the term has been fully expanded to show all child term s S d Male Urogenital Diseases 12 nodes E Genital Diseases Male 4 nodes fl Urogenital Abnormalities 2
5. hen using this workflow Select Apps gt MetScape gt Build Network Select Human from the dropdown menu next to Organism Under the Compounds section click Add In the Add Compounds window enter Glycine and click OK ae a I In the Select Compound Mappings window make sure Glycine is chosen under Potential Matches and click OK 6 Onthe MetScape tab under Options and Network Type use the dropdown menu to select Compound Reaction Enzyme Gene 7 Click Build Network Page 3 of 10 8 Legend Compound Reaction Enzyme Gene Input Significant Up regulated Go to the Opening MetDisease section to begin annotating this network with the MetDisease app The database identifier for this network is KEGG Id Opening MetDisease 1 2 3 Select Apps gt MetDisease gt Find MeSH Terms The Filter Options dialog box appears There are 3 Database Identifiers to choose from a KEGG b PubChem c Name Choose the Database Identifier used in the built network Using the dropdown menu under Select Attribute choose the appropriate column from the input file that contains the identifier Click OK Page 40f 10 Filter Options Identifier Type 7 After the mapping completes the disease branch of the MeSH tree is displayed Go to the MeSH Tree section of this document for more information about the tree MeSH Tree 1 The disease branch of the MeSH tree is displayed in the MetDisease tab in the Cytosc
6. nternal service to access this database via SQL queries in order to determine relevant MeSH disease terms for the compounds in a given metabolic network Workflow 1 Running MetDisease with a User Imported Metabolic Network A network must be built in Cytoscape before using the MetDisease app Example Data Users can import a metabolic network into Cytoscape and then use MetDisease For the imported network example in this User Manual a network was created in Cytoscape using a publicly available metabolomics data set Krumsiek et al 2012 A subset of known metabolites was downloaded from supplementary data Adjusted partial correlation coefficient values less than 5e 4 were used to draw the edges in the resulting network Metabolites are represented as nodes and partial correlation coefficients are represented as edges You can download this sample input file at http metdisease ncibi org Fig 1 network xgmml Page 2 of 10 Go to the Opening MetDisease section to begin annotating this network with the MetDisease app The database identifier for this network is PubChem Id Workflow 2 Running MetDisease with a Network Created Using the MetScape App A network must be built in Cytoscape before using the MetDisease app Example Data For the MetScape created network example in this User Manual a network was created based on the compound Glycine using the MetScape app in Cytoscape The MetScape app must be installed in Cytoscape w
7. rmatics network visualization tool The app is used to annotate a metabolic network with MeSH disease terms explore related diseases within a network and link to PubMed references corresponding to any network node and selection of MeSH terms MeSH terms are controlled vocabulary terms used by the National Library of Medicine to describe the content of the articles indexed in PubMed Users can import and annotate any network where metabolites compounds are represented as nodes referenced by KEGG or PubChem IDs The edges can be arbitrarily defined by the users MetDisease allows users to highlight and explore parts of metabolic networks related to one or more MeSH disease terms and provides links to relevant PubMed literature Users have an option to import their own metabolic networks or to use MetDisease to annotate metabolic networks generated with the Cytoscape app MetScape Gao et al 2010 Karnovsky et al 2012 Note This app requires Cytoscape 3 0 or higher to run correctly Data Source MetDisease uses the Metab2MeSH database Sartor et al 2012 This data set is created twice a year by downloading the PubChem Compound and Substance databases and the NLM PubMed database parsing them and loading them into an in house relational database Associations between compounds and MeSH terms are calculated using two sided Fisher s exact tests and any results with p value lt 0 0001 are retained in the database MetDisease then uses an i
8. s Sarcesine chemistry 1067 0 00e 1 0 00e 1 6070 Barcogineg 3 1088 Chemicals and Drugs Glycine pharmacelogy 225 3 09300 3 434296 50 3 darcosing S 1088 Chemicals and Drugs Glycing Plasma Membrane Transport antagonists amp 68 2 340184 2 09e 180 1140 Erotains inhibitors gareozing 1088 Chemicals and Drugs Detergents a 118 7 31le 172 4 98e 168 692 Technology Industry Agriculture Search by MeSH Terms Use the Cytoscape search box to find nodes that are associated with a specific MeSH term 1 Enter a MeSH term in the Cytoscape search box at the top right of the window Hit the Enter key on your keyboard 2 The nodes associated with this MeSH term are now highlighted in the network Session New Sessioni Bez File Edit View Select Layout Apps Tools Help m ot AE aa A E kA ia kaata E ns Control Panel E a J Compound Reaction Enzyme Gene A oeol pT ee ay Te Nemork oper ts meteno Network Mio Esc sa Compound Aieaction Enz Compound Reaction 118 7 130 Note When doing a search using Cytoscape s search box it searches across all available attribute information not just the MeSH terms As a result additional nodes may become highlighted To Page 9 of 10 narrow the search use quotation marks around phrases ex hepatitis d or nephritis hereditary to ensure that Cytoscape searches for the terms as a phrase References Gao J et al 2010 Me
9. tscape a Cytoscape plug in for visualizing and interpreting metabolomic data in the context of human metabolic networks Bioinformatics 26 7 971 973 PMID 20139469 PMCID PMC2844990 Karnovsky A et al 2012 Metscape 2 bioinformatics tool for the analysis and visualization of metabolomics and gene expression data Bioinformatics 28 3 373 380 PMID 22135418 PMCID PMC3268237 Krumsiek J et al 2012 Mining the unknown asystems approach to metabolite identification combining genetic and metabolic information PLoS Genetics 8 10 e1003005 PMID 23093944 PMCID PMC3475673 Sartor M A et al 2012 Metab2MeSH annotating compounds with medical subject headings Bioinformatics 28 10 1408 1410 PMID 22492643 PMCID PMC3348562 Page 10 of 10
10. y 20 per page Sorted by Recently Added Send to Article types Clinical Trial Review More Results 1 to 20 of 28 Page 1 of2 Next gt Last gt gt oy LEEN Nuclear magnetic resonance based metabolomics enable detection of the effects of a whole grain rye and rye bran diet on the metabolic profile of plasma in prostate cancer patients Text availability Abstract available Free full text available Full text available Publication dates 5 years 10 years Custom range Moazzami AA Zhang JX Kamal Eldin A Aman F Hallmans G Johansson JE Andersson SO J Nutr 2011 Dec141 12 2126 32 doi 10 3945 jn 111 148239 Epub 2011 Oct 19 PMID 22013201 PubMed indexed for MEDLINE Free Article Related citations Is sarcosine a biomarker for prostate cancer issaq HJ Veenstra TD J Sep Sci 2011 Dec 34 24 3619 21 doi 10 1002 jssc 201100572 Epub 2011 Oct 19 PMID 22009695 PubMed indexed for MEDLINE Related citations Accessing Related MeSH Terms Click on a term in the MeSH term tree to highlight its mapped compound s in the drawn network Page 7 of 10 Sarcosing dehydroge lt 7 30036 S ansferase J Hide Unmatched Terms Find MeSH Terms Glycine N Table Panel Male Urogenital Diseases 12 nodes D Y Genital Diseases Male 4 nodes E Eye Diseases 6 nodes Urogenital Abnormalities 2 nod Urogenital Neoplasms 3 nodes 5 Genit
Download Pdf Manuals
Related Search