22nd August 2014
- Ensembl 76 / Ensembl Genomes 23 gene annotations and array design probe set mappings;
- 709 experiments, including 39 RNA-seq experiments (13 baseline, 26 differential), studying samples in 1684 differential comparisons and 24 organisms (see below for breakdown of comparisons per organism);
- All Human RNA-seq experiments have been re-analysed against the new assembly (GRCh38), e.g. RNA-seq of coding RNA from tissue samples of 95 human individuals representing 27 different tissues;
- Baseline expression levels available for genes and transcripts in 75 tissues, 21 cell lines, 7 cellular components, 39 developmental stages and 3 RNA types;
- Quality control reports, e.g. FASTQ QC and Mapping, are now available for all RNA-seq experiments;
- EFO-based autocomplete for experimental conditions is now available on the main Atlas search page. Please see 'How to search' section of Atlas help page for more details. The main search interface also now allows users to restrict search to a single organism;
- User queries in the main Atlas search interface are expanded using the latest EFO. This means that if you search for e.g. "cancer", you will also see results with terms such as "carcinoma", "malignant tumour", and other synonyms and children of the cancer entry in EFO;
- Gene set enrichment analysis (GSEA) is performed using the Piano package from Bioconductor. In each differential experiment, for each contrast, enrichment of terms from GO, InterPro, and Reactome is tested for within the set of differentially expressed genes, using a variation on Fisher's exact test. Plots showing maximum top ten GO, Interpro and Reactome terms enriched within the differentially expressed genes for each contrast are now available for each differential experiment in Atlas. Please see Differential Atlas help for more information.
- For differential expression experiments in Expression Atlas, you can now download a file containing the expression data and meta-data that you can load into R. Please see Expression Atlas data in R help for more information;
- Differential and Baseline Expression can now be visualised on Ensmebl and Ensembl Genomes Genome Browser. Please see Visualising baseline expression at Ensembl and Visualising differential expression at Ensembl for more information.
10th April 2014
- Ensembl 75 / Ensembl Genomes 22 gene annotations and array design probe set mappings;
- 401 experiments, including 24 RNA-seq experiments (8 baseline, 16 differential), studying samples in 19 species and 653 differential comparisons (see below for breakdown of comparisons per experimental factor);
- Average number of citations per experiment: 42 (courtesy of Europe PubMed Central);
- Baseline expression levels available for genes and transcripts in 54 tissues, 21 cell lines, 5 cellular components, 5 developmental stages and 3 RNA types;
- RNA-seq of coding RNA from tissue samples of 95 human individuals representing 27 different tissues data set is now available;
- Automatic quality control (QC) for Microarray experiments in operation; QC reports available to users, e.g. Transcription profiling by array of human PMA-activated MM6 cells with cyclin T1 knockdown
5th December 2013
Welcome to the new Expression Atlas service! The old Expression Atlas and its underlying data will no longer be updated or maintained, but limited support will be offered while the process of re-curation, re-analysis and transferring of experiments to the new Expression Atlas is on-going.
We would like to thank our users for their continuous support, and encourage them to help us shape the new Expression Atlas by:
- providing us with feedback via
mailto:firstname.lastname@example.org via the button on the top right hand side of each page;
- contacting us if any experiments of interest are included in the old Expression Atlas, but have not made their way into the new Expression Atlas yet. We will then prioritise their transfer.
Enjoy the new Expression Atlas!