Databrowsers

ImmGen is a multi-center consortium but its work, and the databrowsers that it develops for community use, are supported by a grant administered at Harvard Medical School. It was thus among those affected by the mass termination of NIH grants to Harvard. We hope to reverse this decision, or align alternative funding, but the resource that ImmGen provides to more than 10,000 immunologists worldwide is threatened.
We would be most grateful for short emails of support, sent to ImmgenATgmail.com or to your US Senator (if applicable), or to whoever you think could valuably support the ImmGen mission.
Gene Skyline
The Skyline presents the expression profiles of a selected gene in a chosen group of cell types, in either microarray or ULI RNA-seq data.
Single Cell Profiling
Display Single Cell RNA-seq profiles from immunological organs and cell-types, and their distinguishing gene modules.
Human Expression Data
Search the expression profile of a selected gene in a chosen immunological cell-type (Gene Skyline), or browse Single Cell RNA-seq profiles.
MicroRNA
MicroRNA abundance profiles in different immunological cell-types (Qiagen qPCR), viewed by cell-type of by predicted target sites.
Gene Constellation
The Constellation view presents the genes most closely correlated to a chosen gene, grouped by genomic location or secondary correlation.
MyGeneset
See how your gene set is expressed across ImmGen cell-types.
Population Comparison
Performs a comparison of gene expression between 2 cell-types (or groups of cell-types), returns the most differential genes and their statistics.
Chromatin
Chromatin profiles in different immunological cell-types (ChIPseq, ATACseq).
Human/Mouse Comparison
Compares the expression of individual genes in human and mouse immune cell lineages, and their co-regulated gene modules.
Enhancer Networks
The Enhancer Networks databrowser allows users to explore the "Open Chromatin Region" of accessible chromatin (mostly promoters or enhancers) associated with a particular gene within the mouse immune system.
Deep RNAseq
Gene expression profiles from different immunological cell-types by TrueSeq RNA-seq, visualized on the UCSC Genome Browser.
Differential Splicing
Differentially spliced isoforms in different immunological cell-types, from RNA-seq junction analysis and from feature-level microarray analysis.
Genetic variation
A series of comparison tools and tables exploring the variation in gene expression between mouse inbred strains.
Modules and regulators
Interactive display of the modules of co-regulated genes across immunological cell-types, and the transcription factors (TFs) predicted to control them.
Cytokines
Presents the transcriptional signatures of cytokines in different immunocyte lineages, predicted regulatory networks and chromatin rearrangements.


ImmGen Datasets
The ImmGen data and browsers are developed as a general resource for the community, principally supported by funds from NIH/NIAID. Datasets can be downloaded from NCBI’s GEO and SRA data repositories, this searchable table provides links to all ImmGen data series and normalized gene tables.



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