Getting GO annotation for your dataset
description
Transcript of Getting GO annotation for your dataset
![Page 1: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/1.jpg)
Getting GO annotation for your dataset
Fiona McCarthy, Shane Burgess, Susan BridgesThe AgBase Databases, Institute of Digital Biology, Mississippi State University
![Page 2: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/2.jpg)
Getting GO:1. Primary sources of GO: from the GO Consortium
(GOC) & GOC members most up to date most comprehensive
2. Secondary sources: other resources that use GO provided by GOC members
public databases (eg. NCBI, UniProtKB) genome browsers (eg. Ensembl) array vendors (eg. Affymetrix) GO expression analysis tools
![Page 3: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/3.jpg)
GO Browsers
![Page 4: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/4.jpg)
1.1 GO Browsers QuickGO Browser (EBI GOA Project)
http://www.ebi.ac.uk/ego/can search by GO Term or by UniProt ID includes IEA annotationsbeta version in testing: will expand functionality
AmiGO Browser (GO Consortium Project)http://amigo.geneontology.org/cgi-bin/amigo/go.c
gican search by GO Term or by UniProt IDdoes not include IEA annotations
![Page 5: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/5.jpg)
A. GO Browser demonstration
AIM: To demonstrate the QuickGO & AmiGO browsers and how they can be used to find GO, find GO terms
![Page 6: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/6.jpg)
The QuickGO Browser (EBI-GOA)
![Page 7: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/7.jpg)
This site is under development - feedback is being requested to make this resource useful to you.Coming soon: download GO annotations for your dataset.
http://www.ebi.ac.uk/ego/
![Page 8: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/8.jpg)
1. Searching by Protein
Multiple protein IDs can be separated by a space or a comma.
![Page 9: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/9.jpg)
![Page 10: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/10.jpg)
![Page 11: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/11.jpg)
Click on “Home” to start a new search.
![Page 12: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/12.jpg)
Search for a GO Term
![Page 13: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/13.jpg)
![Page 14: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/14.jpg)
![Page 15: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/15.jpg)
![Page 16: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/16.jpg)
Filtering Results
Displays all annotations to the search term and its child terms
![Page 17: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/17.jpg)
Filtering Results
use to filter results use to filter results
![Page 18: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/18.jpg)
Filter by database.
![Page 19: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/19.jpg)
Filter by GO Terms
![Page 20: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/20.jpg)
Filter by GO evidence code.
![Page 21: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/21.jpg)
Filter by taxon.
![Page 22: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/22.jpg)
Click on “Home” to start a new search.
![Page 23: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/23.jpg)
The AmiGO Browserhttp://amigo.geneontology.org/cgi-bin/amigo/go.cgi
![Page 24: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/24.jpg)
1. Searching by Gene Product
Note: does not search for multiple IDs
![Page 25: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/25.jpg)
![Page 26: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/26.jpg)
Information about the gene product.
![Page 27: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/27.jpg)
Links to GO annotations.
![Page 28: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/28.jpg)
Download gene GO annotations.
![Page 29: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/29.jpg)
2. Searching by GO Term
![Page 30: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/30.jpg)
Results can be filtered by ontology.
![Page 31: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/31.jpg)
Find term details by clicking on the term name.
![Page 32: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/32.jpg)
See how the term fits in the ontology by selecting Term Lineage.
![Page 33: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/33.jpg)
![Page 34: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/34.jpg)
![Page 35: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/35.jpg)
Select ‘gene product associations’ to display the GO annotations for your search results.
![Page 36: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/36.jpg)
3. Filtering Results
Annotations can be filtered using drop down windows & selecting “set filters”.
![Page 37: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/37.jpg)
![Page 38: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/38.jpg)
Filtered results can be selected & downloaded as a gene association file.
![Page 39: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/39.jpg)
Downloading ga files
![Page 40: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/40.jpg)
1.2 Gene Association files The gene association (ga) file is used by GO
groups to link GO function to gene products tab-delimited file (smaller files can be viewed by opening in Excel) 15 columns (‘fields’) GO Annotation File Format Guide explains data in each column:
http://www.geneontology.org/GO.format.annotation.shtml
![Page 41: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/41.jpg)
Gene Association files The gene association (ga) file is used by GO
groups to link function (GO) to gene products tab-delimited file (smaller files can be viewed by opening in Excel) 15 columns (‘fields’) GO Annotation File Format Guide explains data in each column:http://www.geneontology.org/GO.format.annotation.shtml
![Page 42: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/42.jpg)
http://www.geneontology.org/GO.current.annotations.shtml
![Page 43: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/43.jpg)
http://www.ebi.ac.uk/GOA/downloads.html
![Page 44: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/44.jpg)
GOC: submitted to GO Consortium via EBI-GOACommunity: includes annotations not yet submitted, not supported (have QC)
![Page 45: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/45.jpg)
B. Gene Association file Demonstration
AIM: To show how to download gene association files.
![Page 46: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/46.jpg)
http://www.agbase.msstate.edu/
Select “Downloads & Statistics link.
![Page 47: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/47.jpg)
Click on “Download” link and choose “Save to disk” option.
![Page 48: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/48.jpg)
Find file on desktop.
![Page 49: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/49.jpg)
Unzip using Winzip.
![Page 50: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/50.jpg)
Open extracted file in Excel.
![Page 51: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/51.jpg)
WARNING: some files are too large to open in Excel.
![Page 52: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/52.jpg)
2. Secondary sources of GO annotation
![Page 53: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/53.jpg)
EXAMPLES: public databases (eg. NCBI, UniProtKB) genome browsers (eg. Ensembl) array vendors (eg. Affymetrix)
CONSIDERATIONS: What is the original source? When was it last updated? Are evidence codes displayed?
Secondary Sources of GO annotation
![Page 54: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/54.jpg)
C. Obtaining GO annotations from Secondary Sources
AIM: Look at how different public resources and tools display GO.
![Page 55: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/55.jpg)
GO annotation obtained for chick GAPDH (P00356) from different sources:
QuickGO (primary source) UniProtKB database NCBI Entrez Gene page Ensembl browser Affymetrix chick array g:profiler gene expression analysis tool
![Page 56: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/56.jpg)
QuickGO
![Page 57: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/57.jpg)
1.
![Page 58: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/58.jpg)
2.
![Page 59: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/59.jpg)
![Page 60: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/60.jpg)
![Page 61: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/61.jpg)
![Page 62: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/62.jpg)
![Page 63: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/63.jpg)
![Page 64: Getting GO annotation for your dataset](https://reader035.fdocuments.in/reader035/viewer/2022062517/56813c7b550346895da614a1/html5/thumbnails/64.jpg)
Comparison of Chicken GAPDH GO annotation obtained from different sources.
GO evidence codes not reported.