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Title: Targeted experimentation to increase functional coverage in omics dataset      
dateReleased:
09-03-2016
description:
To increase the GO coverage of Ecomics, we investigated which new conditions would lead to the most informative transcriptional profiles. We first transcriptionally profiled and included in the compendium 9 KO experiments that we had identified before as being highly informative for both GO coverage and model performance. We assumed that a GO term is represented in the compendium if the compendium has profiles where one or more genes that include that GO term have been perturbed. We identified the gene rank iteratively under the assumption that all genes of higher rank have been perturbed. Based on the resulting ranked list, we performed transcriptional profiling for the top 16 genetic perturbations (in triplicate; 48 profiles total), which led to an increase in coverage by 19.8% for KEGG, 24.3% for BP and 63.9% for MF. Genome-wide expression profiling of 25 single-gene knockouts for BW25113 and its wild-type grown with either LB or M9 media supplemented with glucose (total 87 samples).
privacy:
not applicable
aggregation:
instance of dataset
ID:
E-GEOD-73672
refinement:
raw
alternateIdentifiers:
73672
keywords:
functional genomics
dateModified:
09-12-2016
availability:
available
types:
gene expression
name:
Escherichia coli BW25113
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-73672/E-GEOD-73672.raw.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ebi.ac.uk/arrayexpress/files/E-GEOD-73672/E-GEOD-73672.processed.1.zip
storedIn:
ArrayExpress
qualifier:
gzip compressed
format:
TXT
accessType:
download
authentication:
none
authorization:
none
accessURL: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE73672
storedIn:
Gene Expression Omnibus
qualifier:
not compressed
format:
HTML
accessType:
landing page
primary:
true
authentication:
none
authorization:
none
abbreviation:
EBI
homePage: http://www.ebi.ac.uk/
ID:
SCR:004727
name:
European Bioinformatics Institute
homePage: https://www.ebi.ac.uk/arrayexpress/
ID:
SCR:002964
name:
ArrayExpress

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