31 October 2017
14 August 2017
- First pig baseline RNA-seq data (Sus scrofa):
- All RNA-Seq baseline experiments are displayed using TPMs by default where available. There is a new radio button to switch to FPKMs if desired.
- You can download results from the Gene Set Enrichment results page by clicking on the Download results button on the top right.
- Now you can choose what data to download in the experiment page: the highest expressed genes as displayed in the heatmap, or all results matching your query.
18 May 2017
New Home Page
- We have updated our home page with more useful links to species-specific experiments or other large scale projects.
On-the-fly Gene set overlap analysis
New Experiment Page
- Our experiment pages have been re-organised and updated with a new style of heatmap. See help pages for more details while exploring an example:
1 February 2017
- New mouse embryo data from the Mouse Genetics Project/DMDD project:
- New human baseline expression on prenatal brain tissues from the Human Developmental Biology Resource HDBR:
- Data on cross-experiment, organism part heatmaps can now be filtered by anatomical systems and gene expression. Explore example:
2 December 2016
22 September 2016
- Data on heatmaps can now be sorted by gene and protein expression rank. Explore example:
- Faceted search is now available for keyword-based gene or sample property queries. Explore example queries:
22 June 2016
- This release launches the new style of heatmap on the gene/gene-set page. The changes include:
- resize-able, zoom-able display
- assigning expression levels to low, medium, high
New feature: similar expression patterns
This release of Expression Atlas includes datasets on tomato (Solanum lycopersicum), a new species for us! We now have four baseline experiments, studying fruit development and profiling various tissues:
As well as the above baseline datasets, we can also showcase seven differential expression studies on tomato:
The latest release also sees our first experiment studying baseline
expression in different Arabidopsis
tissues, a new dataset on
tonsil from the BLUEPRINT
Epigenome project as well as updates to the previously-added BLUEPRINT dataset on
haematopoiesis, and RNA-seq data
from Open Targets showing baseline
expression of lung disease cell line models.
Bioconductor package out now
21 April 2016
4 April 2016
28 January 2016
17 December 2015
29 October 2015
14 October 2015
14 September 2015
11 August 2015
2 July 2015
5 June 2015
Ensembl 80 / Ensembl Genomes 26 gene annotations and array design probe set mappings.
We are proud to announce that release contains 1,051 datasets (yes, we did celebrate!), now including:
- In particular, this release contains:
- 67 RNA-seq, of which 29 of these report baseline gene expression, across a total of
16 different organisms;
- 366 reporting expression in plants;
- 1,022 studying samples in 2,704
differential comparisons across 24 different organisms.
31st March 2015
20th March 2015
Ensembl 79 / Ensembl Genomes 25 gene annotations and array design probe set mappings.
- This release contains 932 datasets, including:
- 56 RNA-seq, of which 26 of these report baseline gene expression, across a total of
16 different organisms;
- 258 reporting expression in plants;
- 906 studying samples in 2,291
differential comparisons across 20 different organisms.
- New data sets of note:
Differential expression for RNA-seq data is now calculated using DESeq2 method.
Users searching for a single gene within a baseline experiment are now able to see how expression varies across biological replicates for each condition - by selecting Display variation option. For an example click here.
This is currently a prototype - we welcome any feedback you may have. Please use the feedback button on the top right hand side of all Atlas pages.
27th January 2015
18th December 2014
Ensembl 78 / Ensembl Genomes 24 gene annotations and array design probe set mappings
This release contains 873 datasets, including 50 RNA-seq experiments. 23 of these report baseline gene expression, across a total of 16 different organisms. 850 datasets study samples in 2,121 differential comparisons across 20 different organisms.
Please note that splice variant expression quantification is no longer available in Atlas. We have also replaced Cufflinks2 with HTSeq for gene expression quantification.
By clicking on the link highlighted on the image below, the experiment data can now by filtered by gene/protein keywords that were mined from the supporting publication by Europe PubMed Central.
Click here to try it out.
19th November 2014
Ensembl 77 / Ensembl Genomes 24 gene annotations and array design probe set mappings
This release contains 844 datasets, including 50 RNA-seq experiments. 22 of these report baseline gene expression, across a total of 16 different organisms. 822 datasets study samples in 2,032 differential comparisons across 20 different organisms.
Plant experiments, for example our first RNA-seq maize data set, now allow users to display expression in the genome browser.
13th October 2014
Ensembl 77 gene annotations and array design probe set mappings.
This release contains 802 datasets, including 47 RNA-seq experiments. 21 of these report baseline gene expression, across a total of 15 different organisms. 781 datasets study samples in 1,937 differential comparisons across 20 different organisms.
Gene pages now show a combined comparative view for gene expression across multiple baseline datasets.
Hierarchical clustering of the top 100 most variably expressed genes is now performed for each baseline dataset.
Three new anatomograms are now available, for Anolis carolinensis, Xenopus tropicalis and Tetraodon nigroviridis.
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 1,684 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 overlap analysis is performed using the Piano package from Bioconductor. In each differential experiment, for each comparison, enrichment of terms from GO, InterPro, and Reactome is tested for within the set of differentially expressed genes, using Fisher's exact test. Plots showing maximum top ten GO, Interpro and Reactome terms enriched within the differentially expressed genes for each comparison 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 Ensembl and Ensembl Genomes Genome Browser. Please see Visualising baseline expression at Ensembl and Visualising differential expression at Ensembl for more information.
10th April 2014
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:email@example.com or 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!