Objective. Background

Transcription

1 Section E. Host Factor Data Objective Upon completion of this exercise, you will be able to use the Influenza Research Database (IRD; and Virus Pathogen Resource (ViPR; to: Search for host factor experiments using the faceted search function Investigate detailed metadata describing individual experiments Explore pre-computed host response patterns within a given experiment Compare biosets using Boolean Operations Save searches to the Workbench Save results to the Workbench Download data and use it in downstream analyses Perform host factor GO and pathway enrichment analysis Background From its inception in March 2012, the Host Factor data component has been shared between the Influenza Research Database (IRD) and Virus Pathogen Resource (ViPR) in order to support analysis of host responses to human pathogen infection. Currently available host factor data is derived from multiple experiments involving influenza A H1N1 pandemic or seasonal virus, avian influenza A H5N1 virus, SARS-CoV, and MERS-CoV infections in human cell lines and in experimental animals. The data and associated metadata captured in IRD/ViPR fall into three levels: Study: study metadata includes description of the study, PI, point of contact, publications, etc. Experiment: each study is comprised of one or more experiments. Experiment associated metadata includes experiment name, type, measurement technique, experimenters, conditional variables, host species, protocols, etc. Bioset: each bioset contains a list of host factors typically generated by comparing host responses in virus-infected samples with mock-infected samples under different conditions (strain, time point, dose, etc.). 43

2 Workflow Search for Host Factor Experiments: - Use faceted search to find experiments of interest - Explore information about individual experiments Explore Host Response Patterns: - Explore pre-compiled host response patterns on the Experiment page - Search patterns for host factors of interest - Conduct GO enrichment analysis on a pattern - Build working sets from patterns on the Experiment page Use Workbench to Manage Data and Conduct Analyses: - Save host factor data to the Workbench - Perform Boolean operations on host factor working sets Visualize and Conduct Enrichment Analyses: - Output data for downstream visualization and analysis - Conduct GO and pathway enrichment analysis in an external resource 44

3 I. Search for Host Factor Experiments and Compare Biosets 1. Search for host factor experiments using faceted search terms a. To access the host factor experiments, mouse-over the Search Data tab and click the Host Factor Experiments option from the pull down menu. b. The Host Factor Experiment landing page is organized into two panels: a faceted navigation menu on the left, and a table of filtered host factor experiments on the right. The facets allow for quick and efficient data filtering using various structured metadata. c. Now search for host factor experiments using one or more facets. Select the checkbox(es) next to the facet(s) of your interest. In this exercise, we are going to select Orthomyxoviridae under the Family header. This will trigger the table to dynamically update and display the experiments available for this family. Next, select a specific Viral Agent VN1203 (H5N1). The table on the right will now display all experiments that use this strain. 2. Access detailed metadata describing individual experiments a. In the returned table, click ICL004-R in the Experiment ID column. b. You will be taken to the Host Factor Experiment [IRD_SV_ICL004-R] page. Here you can view the Experiment Information, Experiment Sample Summary, Host Factor Bioset Information, Host Factor Bioset Summary, Host Factor Bioset Patterns, and Host Factor Results. 45

4 3. Explore pre-computed host factor bioset patterns a. From the Host Factor Experiment page, scroll down to Host Factor Bioset Patterns, which contains a summary table of statistically significant host factors grouped by expression patterns. Note the patterns that contain the largest numbers of host factors. Click the hyperlinked number in the first row/column to view the list of factors having the selected pattern, together with the fold change and statistical support values. b. Now search for the interferon beta gene and find its expression pattern in experiment ICL004-R. To do so, return to the Host Factor Experiment [IRD_SV_ICL004-R] page by clicking the breadcrumb, type IFNb in the Symbol search box within the Host Factor Bioset Patterns section, and click the Find button. 46

5 c. The expression patterns containing IFNb will be returned in the table below the Find box. What is the expression pattern for this gene? Does it match your expectation? To explain the pattern, we will need to look at the experimental results. d. Now click on the hyperlinked pattern (0,0,+,+,+,+), which will take you to the Experiment Results Details page. e. The Experiment Result Details page displays host factors and associated experimental results. You can select host factors and save them to a working set by clicking Add to, save the search to your Workbench so that you can rerun the same search at a later time, download data and associated metadata, or perform enrichment or pathway analysis. f. Next, click the select all box above the table and then the Download button to download the experiment results. g. In the Download Options box, select Special Tab Delimited - Displayed Columns Only, name the file ICL004-R IFNb pattern, and then click Download. 47

6 4. Perform host factor GO enrichment analysis a. From the Experiment Result Details page for expression pattern (0,0,+,+,+,+), make sure the Select all box above the table is checked, mouse over Run and click Enrichment. b. The Enrichment Algorithm and Gene-Annotation Collection page will be displayed. Select the following options and then click Run. Enrichment Algorithm: CLASSIFI; Gene-Annotation Collection: Gene Ontology (GO); Gene- Annotation Background: From Experiment. 48

7 c. The Enrichment Result page gives the terms, the collections (GO domains in this case), and the p-values calculated by the CLASSIFI algorithm using a hypergeometric distribution function. A selection of results is shown below. d. Select the first term by ticking the corresponding checkbox and click View Term Contents. e. A list of host factors annotated with this GO term will be displayed. 49

8 II. Compare Host Responses to MERS-CoV and SARS-CoV Infections This exercise is based on: Josset, L., et al. (2013) Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus. mbio, 4(3): e MERS-CoV and SARS-CoV are members of the Coronaviridae, a family of enveloped, positive-stranded RNA viruses. Both viruses belong to the Betacoronavirus genus; however, MERS is closer to Bat HKU 4 or 5 (Lineage 2C) than SARS-CoV: they share 50% amino acid identity in the conserved replicase domains. Both viruses cause severe respiratory infections in humans with relatively high mortality frequencies: MERS at ~30%, and SARS at ~10%. These viruses bind to different receptors, specifically, SARS binds to ACE2, while MERS binds to Dipeptidyl peptidase 4 (DPP4). Although these receptors are conserved across many species, most Coronaviridae viruses have limited host range. Now we will compare the host responses to MERS-CoV and SARS-CoV infections to determine which host pathways show a shared response to these two severe respiratory pathogens. a. Navigate back to the Host Factor Experiments page. (Note: If using breadcrumb, prior selections will be remembered. Please deselect ICL004-R before proceeding.) b. Search for experiments containing MERS-CoV or SARS-CoV by selecting the following facets: Family: Coronaviridae; Viral Agent: MERS-CoV, icsars-cov Urbani; Analyte Type: Transcript Quantification c. Next, right-click (Command-click for Macs) on the experiment IDs for ECL001-R and SCL005-R, which were performed under similar conditions, and open them in new tabs. d. On the individual Host Factor Experiment pages, scroll down to the Host Factor Bioset Summary section. How are the host responses to these viruses different at the bioset level? Are the early responses different? Do the peak responses occur at similar times and/or to a similar magnitude? e. Next, we will compare the pattern trends between peak responses for MERS-CoV and SARS-CoV infections. Return to the Host Factor Biosets page, select ECL001_EMC_24h_array_DE and click Patterns above the table. f. The Host Factor Patterns page displays the pattern of the selected bioset. Click on the hyperlinked number corresponding with (+), which stands for up-regulation. g. This will take you to the Experiment Results Details page where it lists all host factors for the selected criteria. 50

9 Virus Pathogen Database and Resource (ViPR) - Flaviv... h. In order to compare the host factors from this pattern to those from another experimental pattern, we will need Flaviviridae to save the host factors to a working set. To do so, check the Select all checkbox at the top of the page, click Add to About Us Community Announcements located Links above Resources the Support table, then in the light SEARCH box, DATA name ANALYZE it MERS & VISUALIZE peak WORKBENCH + and click SUBMIT Save. DATA VIRUS FAMILIES You are logged in as yun.zhang@jcvi.org ViPR Home Flaviviridae Home Host Factor... Host Factor... Host Factor Patterns Host Factor Results Experiment Result Details For each host factor that exceeds the differential expression criteria defined in the experimental protocol, the Fold Change value and adjusted p-value or q-value is shown in the corresponding table cell. Otherwise, the cell is blank. Displaying 500 of 7,741 records. Select all 7,741 records (including those not displayed) Data sorted by Symbol, Host Factor ID in ascend order Your Selected Items: 7,741 items selected Deselect All Add to Save Search Download Download Reactome Data Pathway View HOST FACTOR ID OR SYMBOL Find data for Use comma to separate multiple entries. Ex. DDX58 Reset Associated Bioset Information 1 Study Name ECL001: MERS-CoV infection in Calu3 cells: A time course Experiment Name ECL001-R: MERS-CoV infection in Calu3 cells: A time course Bioset Criteria passes Agilent QC flag and FC > 1.5 and q-value <.05 ECL001-R MERS-CoV, 24 hours, 5 MOI, Calu3 cells Symbol Name Immport Host Factor ID Entrez Gene ID Public Identifier Bioset Information Key Log2 FC P-Value A1CF apobec1 complementation factor A_23_P NM_ A2BP1 ataxin 2-binding protein 1 A_24_P NM_ A2ML1 alpha-2-macroglobulin-like 1 A_23_P NM_ AADAC arylacetamide deacetylase (esterase) A_23_P NM_ i. Repeat AADACL1 the above arylacetamide steps deacetylase-like for bioset 1 SCL005-R_48_WT A_23_P and NM_ save the host 1 factors into 3.2a working set AADAT aminoadipate aminotransferase A_23_P NM_ named SARS peak +. AANAT arylalkylamine n-acetyltransferase A_23_P NM_ AASDH aminoadipate-semialdehyde A_24_P NM_ j. Click Workbench dehydrogenase in the gray navigation bar to access items saved in the Workbench area. AASDHPPT A_23_P NM_ aminoadipate-semialdehyde dehydrogenase- k. In the Workbench phosphopantetheinyl table, select transferasethe two working sets you just created, and then click on More AASDHPPT A_24_P NM_ Actions. aminoadipate-semialdehyde dehydrogenasephosphopantetheinyl transferase AATK apoptosis-associated tyrosine A_23_P NM_ l. This will bring kinase up the More Actions light box, click Intersect and name the new working set ABCA1 atp-binding cassette, sub-family a A_24_P NM_ intersect + MERS SARS. ABCA10 (abc1), member 1 atp-binding cassette, sub-family a (abc1), member 10 A_23_P NM_ ABCA11P ABCA12 ABCA13 atp-binding cassette, sub-family a (abc1), member 11 (pseudogene) atp-binding cassette, sub-family a (abc1), member 12 atp-binding cassette, sub-family a (abc1), member 13 A_23_P NR_ A_23_P NM_ A_23_P NM_

10 Virus Pathogen Database and Resource (ViPR) - Flaviv... SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA VIRUS FAMILIES You are logged in as yun.zhang@jcvi.org ViPR Home Flaviviridae Home My Workbench My Workbench View workbench tutorial: Video Tutorial Tutorial View workbench tutorial: Download Video Tutorial Download Tutorial data of selected working set The workbench lets you store and retrieve various content types in private workspaces, including: working sets (e.g. segments, prot Copy Copy selected working sets uploaded files. Workbench items can be shared with selected collaborators with workbench accounts. Custom workbench The folders workbench ar lets you store and retrieve various content types in private workspaces, including: working sets (e.g. segments, proteins), saved searches, analysis results, and Combine Combine selected working sets into a new working set Display of workbench items can be restricted by content type, access privileges, and organizational folder using the checkboxes uploaded files. on Workbench items can be shared with selected collaborators with workbench accounts. Custom workbench folders are made available to organize content. Intersect Create intersection of selected working sets into a new working set Display of workbench items can be restricted by content type, access privileges, and organizational folder using the checkboxes on the left side of the page. Workbench tutorials, in either video or pdf formats, provide more information on how to use these features. Workbench tutorials, in either Create video Group or pdf formats, provide Add a more collaborator information group on how to use these features. Content s Searches Results Uploaded Files Access Private Shared by me Shared with me Public Flaviviridae Your Selected Items: 2 items selected Deselect All s Sharing Folders Move To Trash More Actions Sharing Folders Move To Trash More Actions UNAVAILABLE ACTIONS Searches Only certain actions are available to you for the items selected. To utilize the disabled actions, please Displaying go back 20 records and select per different page items. Display tings Displaying 20 Results records per page Display tings Uploaded Files Subtract Select all 57 items Create a new working set by subtract one working set from another Next > Page: 1 of 3 Select all 57 items About Us Community Announcements Links Resources Support Name ECL001-R 24h peak response + SCL005-R 48hr peak response + DENV 4 serotype groups Asia Content Type Convert Convert the selected working set into a new working set with different type Access Next > Page: 1 of 3 Content Name Data Type Items Folder Access Date Modified Combine with Uploaded File Combine the selected Type working set with an uploaded sequence Private Combine with ECL001-R 24h Combine peak the selected sequence Host set with Factor a working 7741 set -N/A- Private 2/23/2014 Data Type Items Shared Folder by me Access Date Modified response + 6:56 PM EST Unsubscribe Searches Unsubscribe selected searches from your workbench Shared with me SCL005-R 48hr peak Host Factor N/A- Private 2/23/2014 Host Factor 7741 Public -N/A- Save Private Unsaved Searches 2/23/2014Save selected unsaved searches to your workbench response + 6:53 PM EST Save Unsaved 6:56 PM EST Save selected unsaved analysis result(s) to the workbench Pending Public DENV 4 serotype groups Metadata -N/A- -N/A- Private 2/21/2014 Host Factor N/A- Private Asia 2/23/2014 Special Close 6:53 PM EST Unsaved DENV 4 serotype groups Metadata -N/A- -N/A- Private 2/21/2014 Metadata -N/A- Starred -N/A- Only Private America 2/21/2014 Trash Virus Protein 291 -N/A- Private 2/21/2014 DENV1-4 NS1 America Folders m. After the intersected working set is created, click View next to the working set name in the DENV 4 serotype groups Metadata -N/A- -N/A- Private 2/21/2014 Home Folder DENV1-4 NS1 Asia America Workbench table. Workbench Tutorial WNV-Chimera Uploaded DENV1-4 NS1 America Virus Protein 291 -N/A- Private 2/21/2014 WNV US Africa n. On Details DENV1-4 NS1 page, Asia select all Virus records Protein 411 by -N/A-checking Private the checkbox 2/21/2014 above the table, click Download. WNV-Chimera Nucleotide -N/A- -N/A- Private 2/20/2014 DENV 2 genome WNV US Africa Uploaded File Genome 43 -N/A- Private Dengue 2/20/ human Nov2013 DENV2 polyprotein o. The resulting file is WNV Excel compatible US Africa Tree and will -N/A- be -N/A- used to Private demonstrate /14/2014humandownstream off-site Dengue 2 poly Metadata DENV2 polyprotein MSA JalView -N/A- -N/A- Private Brazilian 12/3/2013 vs Nicaraguan analyses that can be performed. DENV 2 genome tree Tree -N/A- -N/A- Private 11/25/2013 Dengue 2 poly human Dengue 2 human Genome 34 -N/A- Shared By Me Dengue 11/8/2013 NS1 protein Metadata p. Next we will use the downloaded file to conduct an enrichment analysis. betwen 4 serotypes Open Nov2013 the downloaded DENV2 polyprotein Virus Protein 26 -N/A- Private Dengue 6/5/2013 NS1 protein file in Excel, sort the file human on Column C (Entrez gene ID), copy all IDs to the clipboard (don t Dengue Dengue 2 poly Metadata -N/A- -N/A- Private 6/4/2013 worry about duplicates), and then go to Brazilian vs Nicaraguan genome Dengue 2 poly Virus Protein 34 -N/A- Shared By Me 6/4/2013 human q. On the DAVID site, select the Functional Annotation tool on the left bar. Then proceed to upload Dengue NS1 protein Metadata -N/A- -N/A- Private 6/3/2013 betwen 4 serotypes data by choosing the tab Upload. Next, paste your list in the A: Paste a list field, select Dengue NS1 protein Virus Protein 728 -N/A- Private 6/3/2013 ENTREZ_GENE_ID from the Select Identifier pull down, and then select Gene List From Dengue Genome 75 -N/A- Private 5/1/2013 the List Type. Finally, click Submit and DAVID will run an enrichment analysis. genome Dengue 1-4 full genome human MSA Virus Pathogen Database and Resource (ViPR) - Flaviv... SEARCH DATA ANALYZE & VISUALIZE WORKBENCH SUBMIT DATA VIRUS FAMILIES You are logged in as yun.zhang@jcvi.org More Actions My Workbench AVAILABLE ACTIONS ViPR Home Flaviviridae Home My Workbench Muscle -N/A- -N/A- Private 4/30/2013 r. The pathway enrichment shown below demonstrates that the shared overlap between peak responses to SARS-CoV and MERS-CoV is comprised of immune response signaling pathways. 1 of 2 2/23/14 4:51 PM Content Flaviviridae Upload File Edit Group Upload a file About Us Community Announcements Links Resources Support Edit a collaborator group Your Selected Items: 2 items selected Deselect All File Search Workbench Virus Protein 411 -N/A- Private 2/21/2014 Nucleotide -N/A- -N/A- Private 2/20/2014 Genome 43 -N/A- Private 2/20/2014 WNV US Africa Tree -N/A- -N/A- Private 2/14/2014 DENV2 polyprotein MSA JalView -N/A- -N/A- Private 12/3/ tree Dengue 1-4 full genome human MSA Tree -N/A- -N/A- Private 11/25/ Genome 34 -N/A- Shared By Me 11/8/2013 Virus Protein 26 -N/A- Private 6/5/2013 -N/A- -N/A- Private 6/4/2013 Virus Protein 34 -N/A- Shared By Me 6/4/2013 -N/A- -N/A- Private 6/3/2013 Virus Protein 728 -N/A- Private 6/3/2013 Genome 75 -N/A- Private 5/1/2013 Muscle -N/A- -N/A- Private 4/30/ of 2 2/23/14 4:10 PM 52

11 References Li C, et al Host Regulatory Network Response to Infection with Highly Pathogenic H5N1 Avian Influenza Virus. J. Virol. 85: doi: /jvi Huang DW, et al Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Res. 37:1-13. Huang DW, et al Systematic and integrative analysis of large gene lists using DAVID Bioinformatics Resources. Nature Protoc. 4: Josset L, et al Cell Host Response to Infection with Novel Human Coronavirus EMC Predicts Potential Antivirals and Important Differences with SARS Coronavirus. mbio 4:e doi: /mbio Lee JA, et al Components of the antigen processing and presentation pathway revealed by gene expression microarray analysis following B cell antigen receptor (BCR) stimulation. BMC Bioinformatics. 7:237. doi: / Müller MA, et al Human coronavirus EMC does not require the SARS-coronavirus receptor and maintains broad replicative capability in mammalian cell lines. mbio 3:e doi: /mbio Raj VS, et al Dipeptidyl peptidase 4 is a functional receptor for the emerging human coronavirus-emc. Nature 495: van Boheemen S, et al Genomic characterization of a newly discovered coronavirus associated with acute respiratory distress syndrome in humans. mbio 3:e doi: /mbio Zaki AM, et al Isolation of a novel coronavirus from a man with pneumonia in Saudi Arabia. N. Engl. J. Med. 367: