Searching the ENCODE Portal
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1 Searching the ENCODE Portal Asia- Pacific Bioinforma<cs Conference 2016 San Francisco, California Department of Gene<cs, Stanford University 1
2 Topics for this workshop 1. Ge'ng started and addi1onal resources on the ENCODE portal 2. Faceted browsing and metadata access for assays 3. Keyword searches 4. Access to an individual object s metadata and individual data files 5. Faceted browsing of Biosamples and An1bodies 6. Independent hands- on exercise 2
3 GeKng Started hmps:// About tab points of interest Publica(ons: How ENCODE data is used by members of the consor<um and the general public Data Access and Project Overview: ENCODE consor<um and partnerships with other projects 3
4 GeKng Started Methods tab points of interest Data Standards and Experiment Guidelines: ENCODE s standards and requirements for submikng labs. So>ware and Pipelines: Data processing tools 4
5 GeKng Started Help tab points of interest Ge?ng Started: Data organiza<on and access hmps:// gekng- started Tutorials: hmps:// Links to slides from today s workshop Contact: encode- 5
6 GeKng Started hmps:// gekng- started A good place to start How to browse and facet How to access one file at a <me Bulk download of files ENCODE data model and data organiza<on 6
7 GeKng Started Data tab points of interest Assays: access to data, will be most important Biosamples and An(bodies: Used in assays Annota(ons: Broader biological conclusions 7
8 Faceted Browsing: Experiments Faceted Browsing of Assays Click on Data Assays hmps:// type=experiment Facets are filters Limit to items of interest Facets from the same category can be stacked to combine results (logical OR) Facets from different categories further restrict results (logical AND) 8
9 Keyword Searches Search for Skin Some of these search hits don t contain the word skin 9
10 Keyword Searches using Ontologies skin Parent term epidermis Part of Part of dermis Child term Part of Part of Part of 10 kera<nocyte dermis blood vessel endothelial cell fibroblast of dermis
11 Keyword Searches using Ontologies skin Parent term OBI (for assays): hmp://obi- ontology.org Part of EFO (for cell lines): hmp:// UBERON (for <ssues): hmp://uberon.org/ CL (for epidermis primary cells): hmp://cellontology.org/ hmps:// started/#ontologies Part of dermis Child term Part of Part of Part of 11 kera<nocyte dermis blood vessel endothelial cell fibroblast of dermis
12 Metadata to Data: Experiments Use metadata to find data Filter: RNAseq, ENCODE, mm10 assembly Select an experiment: hmps:// experiments/encsr466kzy/ Note metadata on protocols, replicates, etc. Graph: files are related by processing steps Download files from the graph or a list Not all experiments have the graph yet 12
13 Metadata to Data: Experiments Use metadata to find data Filter: RNAseq, ENCODE, mm10 assembly Select an experiment: hzps:// ENCSR466KZY/ Note metadata on protocols, replicates, etc. Graph: files are related by processing steps Download files from the graph or a list Not all experiments have the graph yet 13
14 Metadata to Data: Experiments Use metadata to find data Filter: RNAseq, ENCODE, mm10 assembly Select an experiment: hmps:// ENCSR466KZY/ Note metadata on protocols, replicates, etc. Graph: files are related by processing steps Download files from the graph or a list Not all experiments have the graph yet 14
15 Metadata to Data: Experiments Use metadata to find data Filter: RNAseq, ENCODE, mm10 assembly Select an experiment: hmps:// ENCSR466KZY/ Note metadata on protocols, replicates, etc. Graph: files are related by processing steps Download files from the graph or a list Not all experiments have the graph yet 15
16 Metadata to Data: Experiments Use metadata to find data Filter: RNAseq, ENCODE, mm10 assembly Select an experiment: hmps:// ENCSR466KZY/ Note metadata on protocols, replicates, etc. Graph: files are related by processing steps Download files from the graph or a list Not all experiments have the graph yet 16
17 Metadata to Data: Roadmap Epigenomics Finding data from different projects Filter: ChIP- seq, Roadmap, primary cell hmps:// ENCSR371FHD/ GEO page for Roadmap data: hmp:// acc.cgi?acc=gsm
18 Metadata to Data: Roadmap Epigenomics Finding data from different projects Filter: ChIP- seq, Roadmap, primary cell hmps:// ENCSR371FHD/ GEO page for Roadmap data: hmp:// acc.cgi?acc=gsm
19 Metadata to Data: Roadmap Epigenomics Finding data from different projects Filter: ChIP- seq, Roadmap, primary cell hmps:// ENCSR371FHD/ GEO page for Roadmap processed data: hmp:// acc.cgi?acc=gsm
20 Faceted Browsing: Biosamples Faceted Browsing of Biosamples Click on Data Biosamples hmps:// type=biosample Filter: Homo sapiens, Tissue, Brain, ENCODE hmps:// type=biosample&organism.scien<fic_name=h omo +sapiens&biosample_type=<ssue&organ_slim s=brain&award.project=encode 20
21 Object Pages: Biosamples Biosample metadata Click View all Select hmps:// ENCBS035OKV/ Note donor metadata Click through to donor hmps:// donors/encdo377oga/ 21
22 Object Pages: Biosamples Biosample metadata Click View all Select hmps:// ENCBS035OKV/ Note donor metadata Click through to donor hmps:// donors/encdo377oga/ 22
23 Browsing An<bodies Faceted Browsing of An<bodies Click on Data An<bodies hmps:// type=an<bodylot Characteriza<on standards hmps:// experiment- guidelines/ Example: filtered on Eligible for new data : hmps:// ENCAB934MDN/ 23
24 Browsing An<bodies Faceted Browsing of An<bodies Click on Data An<bodies hmps:// type=an<bodylot Characteriza<on standards hmps:// experiment- guidelines/ Example, filtered on Eligible for new data : hmps:// ENCAB934MDN/ 24
25 An exercise Search for CTCF 1. Find the number of Experiments targe<ng CTCF 2. How many of them are performed using stem cells? 3. Filter: ChIP- seq, immortalized cell line, postnatal life stage 4. Only one of these experiments has treatment informa<on available- which one? 5. What is the accession for the donor of the biosample for Replicate 1 of the human experiment? 25
26 An exercise Search for CTCF 1. Find the number of Experiments targe<ng CTCF ANSWER:
27 An exercise Click through to the Experiments search page 2. How many of them are performed using stem cells? ANSWER: 5 27
28 An exercise Filter as shown 3. Filter: ChIP- seq, immortalized cell line, postnatal life stage 4. Only one of these experiments has treatment informa<on available- which one? ANSWER: ENCSR000DIR 28
29 An exercise Select experiment ENCSR000DUM 5. What is the accession for the donor of the biosample for Replicate 1 of the human experiment? 29
30 An exercise Select experiment ENCSR000DUM Within ENCSR000DUM, select the accession for the biosample under Biological replicate 1 5. What is the accession for the donor of the biosample for Replicate 1 of the human experiment? 30
31 An exercise Select experiment ENCSR000DUM Within ENCSR000DUM, select the accession for the biosample under Biological replicate 1 Scroll down to the Donor Informa<on sec<on of the biosample object page 5. What is the accession for the donor of the biosample for Replicate 1 of the human experiment? ANSWER: ENCDO232AAA 31
32 The ENCODE Portal: Recap 1. Find tutorials, contact details, and other informa1on on how to use the ENCODE portal 2. Use faceted browsing to select and narrow data to items of interest, including searches for data from partner projects 3. Search for data of interest using keyword searches and iden1fiers 4. Navigate the metadata of a single object and retrieve ENCODE data one file at a 1me 5. Hands- on, independent prac1ce at searching and naviga1ng the portal hzps:// started/ hzps:// Any ques<ons? 32
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