Brad Sherman, MS. (bsherman@mail.nih.gov) Weizhong Chang, PhD. (weizhong.chang@nih.gov) March 27, 2024
•  Overview of DAVID Introduction and history of DAVID ○ The importance of DAVID for scientific community 0 Introduction of DAVID tools • Demo o DAVID tools o DAVID API o DAVID Webservice DAVID Web Address: https://davidbioinformatics.nih.gov/
The Database for Annotation, Visualization and Integrated Discovery (DAVID ) bioinformatics resources consists of an integrated biological knowledgebase and analytic tools aimed at systematically extracting biological meaning from large gene/protein lists thereby providing investigators with the ability to gain an in-depth understanding of the biological themes that are enriched in genome-scale studies. DAVID Web Address: https://davidbioinformatics.nih.gov/ https://davidbioinformatics.nih.gov/content.jsp?file=release.html list in the service.

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■ DAVID Bioinformatics Resources: expanded annotation database and novel algorithms to 1871 2007 better extract biology from large gene lists DW Huang, BT Sherman, Q Tan, J Kir, D Liu, D Bryant, Y Guo, Nucleic acids research 35 (suppl_2), W169-W175 ◾ Identifying biological themes within lists of genes with EASE DA Hosack, G Dennis, BT Sherman, HC Lane, RA Lempicki Genome biology 4, 1-8 2222 2003 ■ DAVID: database for annotation, visualization, and integrated discovery G Dennis, BT Sherman, DA Hosack, J Yang, W Gao, HC Lane, Genome biology 4, 1-11 10321 2003

DAVID Google Scholar
https://scholar.google.com/citations?user=6mBdAXAAAAJ&hl=en&a uthuser=1 Data acquired: 03/21/2024
•  Overview of DAVID o Introduction and history of DAVID o The importance of DAVID for scientific community and for NIH/NIH-sponsored research o Introduction of DAVID tools • Demo o DAVID tools o DAVID Webservice o DAVID API DAVID Web Address: https://davidbioinformatics.nih.gov/

2   U.S. Department of Health & Human Services  〉 National Institutes of Health
Home    Start Analysis    Shortcut to DAVID Tools      Technical Center      Downloads & APIs     Terms of Service      About DAVID  ~   About LHRI                          OvervieW Hot Links The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand the biological meaning behind large lists of genes. These tools are powered by the comprehensive DAVID Knowledgebase built upon the DAVID Gene concept which pulls together multiple sources of functional annotations. For any given gene list, DAVID tools are able to: ■ Identify enriched biological themes, particularly GO terms or  Discover enriched functional-related gene groups ty  Cluster redundant annotation terms  Visualize genes on BioCarta & KEGG pathway maps ■ Display related many-genes-to-many-terms on 2-D view. RY  Search for other functionally related genes not in the list ● List interacting proteins 🌸 Explore gene names in batch ● Link gene-disease associations or Highlight protein functional domains and motifs R Redirect to related literatures RY Convert gene identifiers from one type to another. ☎ And more W  One scientist position available in LHRI   W (Updated on Jan 30, 2024) The Laboratory of Human Retrovirology and Immunoinformatics (LHRI: former LHR), Applied/ Developmental Research Directorate (https://david.nciforf.gov) has investigated drug resistance in people living with HIV/AIDS (PLWHA) in the National Institute of Allergy and Infectious Diseases (NIAID) clincal therapy since 2001 to define salvage or de novo therapies. LHRI has also studied the function of novel anti-viral cytokines (Interluekine-27 and Interferon Lambda-1) and the innate immune responses for developing novel immunotherapies. A Scientist I, Cellular Biologist available to investigated HIV and AIDS-related virus pathogenesis in vitro and HIV translational research using molecular biology, cellula biology, virology, and bioinformatics techniques in our Basic Research Section. DAVID Forum Forum for DAVID users to ask questions, suggest new functions and help other users by answering their questions. FAQ Frequently Asked Questions LHRI Publications Publications of the Laboratory of Human Retrovirology and Immunoinformatics, Frederick National Laboratory for Cancer Research DAVID Publications Publications about DAVID What's New DAVID Statistics • March 11, 2024 DAVID is moving to new URL in NIH domain: https://davidbioinformatics.nih.gov/ . January 12, 2024 New Wikipathways viewer integrated into DAVID with list gene highlighting, searchable pathway gene table, zooming, panning and download capabilities. ●   December 21, 2023 DAVID Knowledgebase v2023q4 released. ●  October 12, 2023 DAVID Web Address: https://davidbioinformatio ● > 69K Citations (Updated 1/12/2024) • Average Daily Usage: −2,700 gene lists/sublists from −900 unique researchers. • Average Annual Usage: ~1,000,000 gene lists/sublists from >100 countries
U.S. Department of Health & Human Services National Institutes of Healt lational Institutes of Health JAVID Bioinformatics Home    Start Analysis    Shortcut to DAVID Tools      Technical Center     Downloads & APIs     Terms of Service     About DAVID     About LHRI                            Upload  List     Background Upload Gene List *** You must upload a gene list before a background *** Step 3: List Type Gene List     O Background O Step 4: Submit List Submit List Gene ID Conversion Tool Help and Tool Manual Option 1: Convert the gene list being selected in left panel to [ official_gene_symbol > For species:   Homo sapiens Submit to Conversion Tool Option 2: Go Back to Submission Form
*** Welcome to DAVID 6.8 *** *** If you are looking for DAVID 6.7, please visit our development site. *** Background Upload 3 Analysis Wizard Gene List Manager Select to limit annotations by one View Unmapped Ids ☞ Step 1. Successfully submitted gene list Current Gene List: demolist2 Current Background: Affymetrix Barley Genome Array Step 2. Analyze above gene list with one of DAVID tools MحFunctional Annotation Tool • Functional Annotation Clustering • Functional Annotation Chart • Functional Annotation Table ← Gene Functional Classification Tool S Gene ID Conversion ToolحGene Name Batch Viewer
Fl

U.S. Department of Health & Human Services National Institutes of Health Health Home    Start Analysis    Shortcut to DAVID Tools      Technical Center     Downloads & APIs     Terms of Service     About DAVID     About LHRI                            Upload Population Manager Analysis Wizard Select a background    Help Affymetrix Exon Backgrounds ☞ Step 1. Successfully submitted gene list Current Gene List: geneList1 Current Background: Homo sapiens Step 2. Analyze above gene list with one of DAVID tools → Functional Annotation Tool ● Functional Annotation Clustering ● Functional Annotation Chart ● Functional Annotation Table ➪ Gene Functional Classification Tool 😊 Gene ID Conversion Tool ➪ Gene Name Batch Viewer Tell us how you like the tool Contact us for questions Which DAVID tools to use?

U.S. Department of Health & Human Services
National Institutes of Health onal Institutes of Health Home    Start Analysis    Shortcut to DAVID Tools      Technical Center      Downloads & APIs     Terms of Service     About DAVID      About LHRI                         
Annotation Summary Results
Current Gene List: demolist1 Current Background: Homo sapiens ■ Disease (2 selected) ● Functional_Annotations (5 selected) ● Gene_Ontology (3 selected) @ Gene_Report_Categories (0 selected) ● General_Annotations (0 selected) ❏ Interactions (1 selected) ❏ Literature (0 selected) ◾ Pathways (3 selected) ● Protein_Domains (4 selected) ® Tissue_Expression (0 selected) 145 DAVID IDs Check Defaults 🌸 Help and Tool Manual Clear All ***Red annotation categories denote DAVID defined defaults*** Combined View for Selected Annotation Functional Annotation Clustering Functional Annotation Chart Functional Annotation Table
National Institutes of Health U.S. Department of Health & Human Services onal Institutes of Health ID Bioinformat Start Analysis Shortcut to DAVID Tools ➤ Technical Center ➤ Downloads & APIs ➤ Terms of Service ➤ About DAVID ➤ About LHRI ➤ Home Upload List Gene List Manager Select to limit annotations by one or more species    Help Select Species List Manager    Help ☞ Step 1. Successfully submitted gene list Current Gene List: geneList1 Current Background: Homo sapiens Step 2. Analyze above gene list with one of DAVID tools ☁ Functional Annotation Tool ● Functional Annotation Clustering ●   Functional Annotation Chart ●   Functional Annotation Table 😊 Gene Functional Classification Tool A ➪ Gene Name Batch Viewer Which DAVID tools to use? Analysis Wizard Tell us how you like the tool Contact us for questions
Gene List Report Help and Manual Current Gene List: demolist1 Current Background: Homo sapiens 145 DAVID IDs
U.S. Department of Health & Human Services National Institutes of Health ational Institutes of Health DAVID Bioinformatics Home   Start Analysis   Shortcut to DAVID Tools 否  Technical Center 否  Downloads & APIs 否  Terms of Service 否  About DAVID 否  About LHRI 否Upload  List  Background Gene List Manager Select to limit annotations by one or more species    Help - Use All Species - Homo sapiens(149) Unknown(15) Select Species List Manager    Help demolist1 View Unmapped Ids Gene ID Conversion Tool Help and Tool Manual Option 1: Convert the gene list being selected in left panel to [ ENTREZ_GENE_ID (Default)   ✔ Homo sapiens For species: Submit to Conversion Tool Option 2: Go Back to Submission Form

Gene Accession Conversion Tool

National Institutes of Health U.S. Department of Health & Human Services utes of Health ID Bioinforma Start Analysis Shortcut to DAVID Tools ➤ Technical Center ➤ Downloads & APIs ➤ Terms of Service ➤ About DAVID ➤ About LHRI ➤ Home Upload List Analysis Wizard Gene List Manager Select to limit annotations by one or more species    Help List Manager    Help demolist1 geneList1 ☞ Step 1. Successfully submitted gene list Current Gene List: geneList1 Current Background: Homo sapiens Step 2. Analyze above gene list with one of DAVID tools Which DAVID tools to use? ☁ Functional Annotation Tool ● Functional Annotation Clustering ●   Functional Annotation Chart ●   Functional Annotation Table Tell us how you like the tool Contact us for questions
National Institutes of Health U.S. Department of Health & Human Services ational Institutes of Health JAVID Bioinformatic Home    Start Analysis    Shortcut to DAVID Tools      Technical Center     Downloads & APIs     Terms of Service     About DAVID     About LHRI                           
Annotation Summary Results
Current Gene List: demolist1 Current Background: Homo sapiens ❏  Disease (2 selected) ❏ Functional_Annotations (5 selected) ❏ Gene_Ontology (3 selected) ❏ Gene_Report_Categories (0 selected) ❏ General_Annotations (0 selected) ❏ Interactions (1 selected)田 Literature (0 selected) ❏  Pathways (3 selected)田 Protein_Domains (4 selected) ❏ Tissue_Expression (0 selected) ***Red annotation categories denote DAVID defined defaults*** Combined View for Selected Annotation Functional Annotation Clustering Functional Annotation Chart Help and Tool Manual
U.S. Department of Health & Human Services      National Institutes of Health tional Institutes of Health AVID Bioinformatics Home    Start Analysis    Shortcut to DAVID Tools      Technical Center     Downloads & APIs     Terms of Service     About DAVID     About LHR Upload  List   Background Gene List Manager
Annotation Summary Results
Select to limit annotations by one or more species    Help - Use All Species - Homo sapiens(149) Unknown(15) Select Species List Manager   Help demolist1 Select List to: Use Rename Remove   Combine Show Gene List /iew Unmapped Ids Current Gene List: demolist1 Current Background: Homo sapiens日 Disease (2 selected) ■ DISGENET □ GAD_DISEASE □ GAD_DISEASE_CLASS 🎁 OMIM_DISEASE 🎁 UP_KW_DISEASE ® Functional_Annotations (5 selected) ❏ Gene_Ontology (3 selected) ❏ Gene_Report_Categories (0 selected) ❏ General_Annotations (0 selected)
145 DAVID IDs Check Defaults 🌸 Clear All Help and Tool Manual 4.1%  6 17.9% 26 25.5% 37 55.9% 81 75.2% 109 56.6% 82 ❏ Protein_Domains (4 selected) ❏ Tissue_Expression (0 selected)
Functional Annotation Chart Help and Manual Current Gene List: demolist1 Current Background: Homo sapiens 145 DAVID IDs ❏ Options Rerun Using Options Create Sublist
U.S. Department of Health & Human Services      National Institutes of Health tional Institutes of Health AVID Bioinformatics Home    Start Analysis    Shortcut to DAVID Tools      Technical Center     Downloads & APIs     Terms of Service     About DAVID     About LHR Upload  List Gene List Manager
Annotation Summary Results
Help and Tool Manual Select to limit annotations by one or more species    Help - Use All Species - Homo sapiens(149) Unknown(15) Select Species List Manager   Help demolist1 Select List to: Use Rename Remove   Combine Show Gene List /iew Unmapped Ids Current Gene List: demolist1 Current Background: Homo sapiens日 Disease (2 selected) ■ DISGENET □ GAD_DISEASE □ GAD_DISEASE_CLASS 🎁 OMIM_DISEASE 🎁 UP_KW_DISEASE ® Functional_Annotations (5 selected) ❏ Gene_Ontology (3 selected) ❏ Gene_Report_Categories (0 selected) ❏ General_Annotations (0 selected)
❏ Protein_Domains (4 selected) ❏ Tissue_Expression (0 selected) 145 DAVID IDs Check Defaults 🌸 Clear All 55.9% 81 75.2% 109 56.6% 82 4.1% 6 17.9% 26 25.5% 37
U.S. Department of Health & Human Services      National Institutes of Health
Functional Annotation Table
Help and Manual Current Gene List: demolist1 Current Background: Homo sapiens 145 DAVID IDs
National Institutes of Health U.S. Department of Health & Human Services Shortcut to DAVID Tools      Technical Center     Downloads & APIs      Terms of Service     About DAVID      About LHI Home    Start Analysis Background Upload  List Analysis Wizard Select Species ∅ Gene ID Conversion Tool令Gene Name Batch Viewer A ⇒ Gene Functional Classification Tool
Tell us how you like the tool Contact us for questions & Step 1. Successfully submitted gene list Current Gene List: demolist1 Current Background: Homo sapiens Step 2. Analyze above gene list with one of DAVID tools Which DAVID tools to use?

Functional Annotation Table
Help and Manual Current Gene List: demolist1 Current Background: Homo sapiens 145 DAVID IDs
4. Services (*) EMBL-EBI EMBL-EBI Overview Synonyms Ancestor Chart
GO:0006569 © © Wison
tryptophan catabolic process Biological Process Definition (GO:0006569 GONUTS page) The chemical reactions and pathways resulting in the breakdown of tryptophan, the chiral amino acid 2-amino-3-(1H-indol-3- yl)propanoic acid.
241,977 annotations
Synonyms
Synonyms are alternative words or phrases closely related in meaning to the term name, with indication of the relationship between the name and synonym given by the synonym scope.

Ancestor Chart 😍
Ancestor chart for GO:0006569     Chart options Child Terms Annotation Guidance GO Discussions Taxon Constraints Blacklist Cross-References Cross-Ontology Relations Replaces Replaced By Co-occurring Terms GO Stims Change Log Search Basket API
U.S. Department of Health & Human Services National Institutes of Health ational Institutes of Health DAVID Bioinforma Home   Start Analysis   Shortcut to DAVID Tools     Technical Center     Downloads & APIs     Terms of Service     About DAVID     About LHRI    
Annotation Summary Results
Current Gene List: demolist1 Current Background: Homo sapiens ■ Disease (2 selected) ☞ Functional_Annotations (5 selected) ■ Gene_Ontology (3 selected) @ Gene_Report_Categories (0 selected) @ General_Annotations (0 selected)画Interactions (1 selected) ● Literature (0 selected) ◾ Pathways (3 selected) ● Protein_Domains (4 selected) ® Tissue_Expression (0 selected) ***Red annotation categories denote DAVID defined default Combined View for Selected Annotation Functional Annotation Clustering Functional Annotation Chart Functional Annotation Table 145 DAVID IDs Check Defaults 🌸 Help and Tool Manual Clear All

Functional Annotation Chart
Current Gene List: demolist1 Current Background: Homo sapiens 145 DAVID IDs ❏ Options Help and Manual
U.S. Department of Health & Human Services National Institutes of Health tional Institutes of Health DAVID Bioinformatics Home    Start Analysis    Shortcut to DAVID Tools      Technical Center     Downloads & APIs     Terms of Service     About DAVID     About LHRI                           
Annotation Summary Results
Current Gene List: demolist1 Current Background: Homo sapiens ● Disease (2 selected) ● Functional_Annotations (5 selected) ❏ Gene_Ontology (3 selected) ■ Gene_Report_Categories (0 selected) ■ General_Annotations (0 selected) ◄ Interactions (1 selected) ▣ Literature (0 selected) ❏ Pathways (3 selected) ●  Protein_Domains (4 selected) ⊕ Tissue_Expression (0 selected) ***Red annotation categories denote DAVID defined defaults*** Combined View for Selected Annotation Functional Annotation Clustering Functional Annotation Chart Functional Annotation Table 145 DAVID IDs Check Defaults 🌸 Help and Tool Manual
Functional Annotation Clustering
Current Gene List: demolist1 Current Background: Homo sapiens 145 DAVID IDs Classification Stringency | Medium ❤日Options Rerun using options Create Sublist 37 Cluster(s)
Help and Manual
230 terms  were not clustered.
Functional Annotation Clustering Current Gene List: demolist1 Current Background: Homo sapiens 145 DAVID IDs日Options Classification Stringency  Medium ❤ Custom Create Sublist Rerun using options
Help and Manual
37 Cluster(s)

2D View
Help ■ corresponding gene-term association positively reported      ■ corresponding gene-term association not reported yet [4] Download File KW-0964~Secreted GO:0005615~extracellular space CARBOHYD:N-linked (GlcNAc...) as: G0:0005576~extracellular region KW-1015-Disulfide bond KW-0325-Glycoprotein KW-0732~Signal Download File
U.S. Department of Health & Human Services National Institutes of Health Home    Start Analysis    Shortcut to DAVID Tools      Technical Center     Downloads & APIs     Terms of Service     About DAVID     About LHRI                            Upload Background List Gene List Manager Select to limit annotations by one - Use All Species - Homo sapiens(149) Unknown(15) Select Species List Manager    Help demolist1 ☞ Step 1. Successfully submitted gene list Current Gene List: demolist1 Current Background: Homo sapiens Step 2. Analyze above gene list with one of DAVID tools Which DAVID tools to use? ⇒ Functional Annotation Tool ● Functional Annotation Clustering ● Functional Annotation Chart B ●  Functional Annotation Table 😊 Gene Functional Classification Tool ➪ Gene ID Conversion Tool - A ☁ Gene Name Batch Viewer_ Analysis Wizard Tell us how you like the tool Contact us for questions

Gene Functional Classification Result
Help and Tool Manual Current Gene List: demolist1 Current Background: Homo sapiens 145 DAVID IDs Medium × ❏ Options Classification Stringency Rerun using options Create Sublist
2
Cluster(s)
11 Download File

from your list are not in the output.

2 Cluster(s)

Functional Related Genes
Search Scope: User's List田 Options Rerun Using Options 145 gene(s) were searched. 15 genes passed the時Download File filter. Very High (0.75-1) High (0.5-0.75) Moderate (0.25-0.5) Low ( <0.25) Similarity Score:
Cluster(s) Ki Download P
Term Report Gene Cluster 1 Current Gene List: demolist1 Current Background: Homo sapiens
2

2D View
Help ■ corresponding gene-term association positively reported     ■ corresponding gene-term association not reported yet   tumor protein p53 inducible protein 11(TP53I11) Fas apoptotic inhibitory molecule 2(FAIM2) immunoglobulin kappa variable 1-13(IGKV1-13) pregnancy specific beta-1-glycoprotein 4(PSG4) uroplakin 1A(UPK1A) CEA cell adhesion molecule 8(CEACAM8) CEA cell adhesion molecule 3(CEACAM3) ADAM metallopeptidase domain 23(ADAM23) neuregulin 2(NRG2) natural cytotoxicity triggering receptor 3(NCR3) neural cell adhesion molecule 1(NCAM1)
DAVID API allows other bioinformatics web sites to directly link to DAVID tools and functions ONLY for light-duty jobs (i.e. a gene list with no more than 400 genes). https://davidbioinformatics.nih.gov/content.jsp?file=DAVID  API.html • DAVID API is not for high-throughput or large gene list jobs, such as a job for a gene list with more than 500 genes or trying to loop through multiple gene lists. These types of uses should use the DAVID Webservice. . The URL has a character size limitation and therefore a very large gene list may not be completely passed in the GET call.
Example API Calls:
Functional Annotation Summary Page: https://davidbioinformatics.nih.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=summary Functional Annotation Chart: https://davidbioinformatics.nih.gov/api.iso?type=ENTREZ_GENE_ID&id=2919,6347,6348,6364&tool=chartReport&annot=GOTERM_BP_FAT.GOTERM_CC_FAT.GOTERM_ME_FAT.INTERPRO.PI R_SUPERFAMILY,SMART,BBID,BIOCARTA,KEGG_PATHWAY,COG_ONTOLOGY,SP_PIR_KEYWORDS,UP_SEQ_FEATURE,GENETIC_ASSOCIATION_DB_DISEASE,OMIM_DISEASE
Functional Annotation Table:
https://davidbioinformatics.nih.gov/apl.isp?type=ENTREZ_GENE_ID&id=2919,6347,6348,6364&tool=annotationReport&annot=GOTERM_BP_FAT,GOTERM_CC_FAT,GOTERM_ME_FAT,INTERP RO,PIR  SUPERFAMILY,SMART,BBID,BIOCARTA,KEGG  PATHWAY,COG  ONTOLOGY,SP  PIR  KEYWORDS,UP  SEQ  FEATURE,GENETIC  ASSOCIATION  DB  DISEASE,OMIM  DISEASE Functional Annotation Clustering: https://davidbioinformatics.nih.gov/api.iso?type=ENTREZ_GENE_ID&id=2919,6347,6348,6364&tool=term2term&annot=GOTERM_BP_FAT,GOTERM_CC_FAT,GOTERM_ME_FAT,INTERPRO,PIR superfamily,smart,88id,biocarta,kegg_pathway,cog_ontology,sp_pir_keywords,up_seq_feature,genetic_association_db_disease,omim_disease Gene Full Report: https://davidbioinformatics.nih.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=geneReportFull Gene Report: https://davidbioinformatics.nih.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=geneReport Show Gene List Names in Batch: https://davidbioinformatics.nih.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364&tool=list Gene Functional Classification: https://davidbioinformatics.nih.gov/api.jsp?type=ENTREZ_GENE_ID&ids=2919,6347,6348,6364,6351&tool=gene2gene
Allows users to programmatically (Java, Perl, Python, R, C, etc) interact with DAVID and automate their tasks. https://davidbioinformatics.nih.gov/content.jsp?file=WS.html ▷Simple Object Access Protocol (SOAP), exchanges XML messages between client and the Service provider (Java, C, Perl, Python, R, Matlab, etc...)
Xiaoli Jiao, Brad T. Sherman, et al. DAVID-WS: A Stateful Web Service to Facilitate Gene/Protein List Analysis Bioinformatics 2012

from suds.client import Client import pandas as pd url = 'https://davidbioinformatics.nih.gov/webservice/services/DAVIDWebService?wsdl' print('url={}'.format(url)) # Create a service client using the wsdl. This only needs to be done once at the beginning of the code. client = Client(url) client.wsdl.services[0].setlocation('https://davidbioinformatics.nih.gov/webservice/services/ DAVIDWebService.DAVIDWebServiceHttpSoap11Endpoint/") #Authenticate user email. This only needs to be done once. client.service.authenticate('bsherman@nih.gov') # Define the input gene list file, identifier type, list type and a list name inputFile = "demolist2.txt" idType = 'AFFYMETRIX 3PRIME IVT ID' listType = 0 listName = "demolist2" # Set the annotation categories of interest and define the EASE and count thresholds for the chart report categorySting = str(client.service.setCategories('OHIM DISEASE,UP KW DISEASE,UP KW BIOLOGICAL PROCESS UP_KW_CELLULAR_COMPONENT,UP_KW_MOLECULAR_FUNCTION, UP_KW_PTM,UP_SEQ_FEATURE,GOTERM_BP_DIRECT, GOTERM CC DIRECT,GOTERM MF DIRECT,UP KN LIGAND,BBID,BIOCARTA,KEGG PATHWAY,INTERPRO,PIR SUPERFAMILY, SMART,UP KW DOMAIN')() thd = 0.05 ct = 2 # Read input gene list file, convert ids to a comma-delimited string and upload the list to DAVID df=pd.read_csv(inputFile, usecols=[0], delimiter='\t', index_col=False, names= ['AFFYMETRIX_3PRIME_IVT_ID']) inputIds = ",".join(df['AFFYMETRIX_3PRIME_IVT_ID'].astype(str).unique().tolist()) client.service.addList(inputIds, idType, listName, listType) # Request a chart report for the input list using the previously set categories chartReport – client.service.getChartReport(thd,ct) numChartRecords = len(chartReport) print('Total chart records:{}'.format(numChartRecords)) # Create a pandas dataframe from the returned chart records dfResults = pd.DataFrame(columns = ['Category','Term','Count','Percent','PValue','Benjamini']) for simpleChartRecord in chartReport: dfResults=dfResults.append({ 'Category':simpleChartRecord.categoryName, 'Term':simpleChartRecord. termName, 'Count':simpleChartRecord.listHits, 'Percent':simpleChartRecord.percent, 'PValue':simpleChartRecord.ease, 'Benjamini':simpleChartRecord.benjamini},ignore_index = True) print(dfResults) https://davidbioinformatics.nih.gov/webservice/services/DAVIDWebService?wsdl
getChartReport
▼<xs:element name="getChartReport"> ▼<XS:complexType> V<XS:sequence> <xs:element name="args0" type="xs:double"/> <xs:element name="args1" type="xs:int"/> </xs:sequence> </xs:complexType> </xs:element> v<xs:element name="getChartReportResponse"> ¥<xs:complexType> V<XS:sequence> <xs:element maxOccurs="unbounded" minOccurs="0" name="re nillable="true" type="ax22:simpleChartRecord"/> </xs:sequence> </xs:complexType> </xs:element>
simpleChartRecord
v<xs:complexType name="simpleChartRecord"> Y<XS:sequence> <xs:element minOccurs="0" name="EASEBonferroni" type="xs:double"/> <xs:element minOccurs="0" name="afdr" type="xs:double"/> <xs:element minOccurs="0" name="benjamini" type="xs:double"/> <xs:element minOccurs="0" name="bonferroni" type="xs:double"/> <xs:element minOccurs="0" name="categoryName" nillable="true" type="xs:string"/> <xs:element minOccurs="0" name="ease" type="xs:double"/> <xs:element minOccurs="0" name="fisher" type="xs:double"/> <xs:element minOccurs="0" name="foldEnrichment" type="xs:double"/> <xs:element minOccurs="0" name="geneIds" nillable="true" type="xs:string"/> <xs:element minOccurs="0" name="id" type="xs:int"/> <xs:element minOccurs="0" name="listHits" type="xs:int"/> <xs:element minOccurs="0" name="listName" nillable="true" type="xs:string"/> <xs:element minOccurs="0" name="listTotals" type="xs:int"/> <xs:element minOccurs="0" name="percent" type="xs:double"/> <xs:element minOccurs="0" name="popHits" type="xs:int"/> <xs:element minOccurs="0" name="popTotals" type="xs:int"/> <xs:element minOccurs="0" name="rfdr" type="xs:double"/> <xs:element maxOccurs="unbounded" minOccurs="0" name="scores" nillable="true" type="xs:double"/> <xs:element minOccurs="0" name="termName" nillable="true" type="xs:string"/> </xs:sequence> </xs:complexType>
url=https://davidbioinformatics.nih.gov/webservice/services/DAVIDWebService?wsdl
records:425
MF 01REC1 RD_DIRECT 8P DIRECT INTERPRO

NIAID, NIH
•  Cliff Lane
Frederick National Laboratory
•  Michael Baseler • LHRI Tomozumi Imamichi Ming Hao Lei Xu Lynn Dotrang Xuan Li Ganesh Panzade • IT Support: •  Sharon Beck •  Bill Wilton •  Shawn Steward
Frederick National Laboratory
•   Advanced Biomedical Computational Science (ABCS) staff: Jack Collins Uma Mudunuri Henri Tuthill Anney Che David Bryant •   Previous DAVID Bioinformatics Team: Richard Lempicki Glynn Dennis Doug Hosack Da Wei Huang Xiaoli Jiao Ju Qiu