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Raw gene Expression data is sourced from GEO, and the appropriate db package for mapping probes to gene symbols was sourced from the Bioconductor AnnotationData packages.
You can read more about microarray data here.
Select conditions below to toggle them from the plot:
| GROUP | CONDITION | SAMPLES |
|---|---|---|
| Mammary Alveolar Cells |
GSM1164975 GSM1164976 GSM1164977
|
|
|
GSM1164972 GSM1164973 GSM1164974
|
Submission Date: Jun 17, 2013
Summary: The floxed insulin receptor was specifically targetted for deletion in the mammary gland using a mouse strain bearing Cre recombinase under the BLG promoter.
Data analysis: Genespring was used for data analysis
All entities (28853) were filtered on variance between samples, eliminating from further analysis of genes whose coefficient of variation was greater than 50%.
The remaining 2239 genes were filtered on expression levels between 20 and 20,000 intensity units
An unpaired T-test was used to find genes that differed significantly (P<0.05) between experimentals and controls
The remaining 2014 genes were filtered for a 1.1 absolute fold change between experimentals and controls.
Of the remaining expression of 890 genes was down in the Cre+ mice and expression was up for 457 genes in the Cre+ mice.
GEO Accession ID: GSE48009
PMID: 23982156
Submission Date: Jun 17, 2013
Summary: The floxed insulin receptor was specifically targetted for deletion in the mammary gland using a mouse strain bearing Cre recombinase under the BLG promoter.
Data analysis: Genespring was used for data analysis
All entities (28853) were filtered on variance between samples, eliminating from further analysis of genes whose coefficient of variation was greater than 50%.
The remaining 2239 genes were filtered on expression levels between 20 and 20,000 intensity units
An unpaired T-test was used to find genes that differed significantly (P<0.05) between experimentals and controls
The remaining 2014 genes were filtered for a 1.1 absolute fold change between experimentals and controls.
Of the remaining expression of 890 genes was down in the Cre+ mice and expression was up for 457 genes in the Cre+ mice.
GEO Accession ID: GSE48009
PMID: 23982156
Visualize Samples
Visualizations are precomputed using the Python package scanpy on the top 5000 most variable genes.
Precomputed Differential Gene Expression
Differential expression signatures are automatically computed using the limma R package.
More options for differential expression are available to compute below.
Signatures:
Select conditions:
Control Condition
Perturbation Condition
Only conditions with at least 1 replicate are available to select
Differential expression signatures can be computed using DESeq2 or characteristic direction.