- mouse (0) (x)
- human (0) (x)
- logFC>=0 (0) (x)
- logFC<0 (0) (x)
- correlation>=0 (0) (x)
- correlation<0 (0) (x)
- score>=0 (0) (x)
- score<0 (0) (x)
Filters
Species
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all / none | Symbol | Synonyms | Description | Expression | Links | Orthologue | Species | logFC | adj P | AveExpr | correlation | score |
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rows per page |
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all genes filtered genes
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You can save this geneset to the server, which enables later retrieval as well as some other functions. Note that filtered list is saved, so remove all filters first if you wish to save the full list of genes.
Geneset Name:
Description:
Show Heatmap
You can see a heatmap of this geneset by selecting a dataset below. It uses the filtered list of genes, so remove all filters if you want a heatmap on all genes.
Number of genes (in filtered list): 0
Species:
Manage Genesets
You can remove a saved geneset here or clear genesets from history.
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Citation: Haemopedia RNA-seq: a database of gene expression during haematopoiesis in mice and humans Nucl. Acids Res. (2019) Version 4.9.5 (2019-02-07) © 2015 Walter and Eliza Hall Institute |
Haemosphere Release Notes
Version 4.9.5 (2019-02-07)
- Updated citation information for publication of Haemoepdia RNA-Seq and new Haemosphere features in Nucl. Acids Res. https://doi.org/10.1093/nar/gky1020
- Corrected Haemopedia Microarray dataset downloads to just be the probes that are supported by our ensembl annotation
Version 4.9.4 (2018-09-25)
- Added tour style help on some pages which can be activated by clicking on the question mark symbol.
- RNA-Seq datasets have tpm instead of rpkm values now.
- Downloading R objects as a file in just after differential expression analysis is now possible (Differential Expression Search -> view the R script -> download R objects).
- Datasets without ordering defined for celltype will now use cell lineage to order columns in heatmaps.
Version 4.9.3 (2018-09-07)
- Fixed a bug where gene vs gene changed both genes if currently showing two same genes.
- Fixed a bug where saving a dataset subset didn't work and caused the same dataset to be inaccessible.
Version 4.9.2 (2018-08-08)
- High expression search now filers lowly expressed and variant genes before scoring.
- Fixed a bug where heatmap wasn't working at all.
- Improved image download for multi-species plot.
- Fixed a bug where sample selection for dataset subsetting was available without a login.
- Updated help text in various places.
Version 4.9.1 (2018-08-02)
- Changed the way dataset attributes are fetched to greatly speed up page loading times.
- A new feature, gene vs gene plot, has been added.
- Multi-species plot is more compact, with less datasets shown as default. The user can select datasets.
- Multi-species plot can show legend and each plot can now be saved as a static image.
- Select bar is now used for functions performed on each row of the gene table and for functions on expression profile page.
Version 4.9 (2018-06-20)
- Removed the login requirement for differential and high expression searches.
- Added a multi-species gene expression plot, where you can see expression of a gene and its orthologue across all datasets.
- Fixed email problem, which affected self-registration and password management.
- Added new datasets.
- Changed the front page to include News page and made it the first landing page.
- Fixed a bug where DE analysis didn't work without a useful message when there were no replicate samples.
- Changed ordering of gene set that comes back after DE analysis so that it's on absolute logFC.
- Changed ordering of datasets.
- Renamed some datasets.
- Geneset page has a new "Expression" column which has links to expression profiles including multi-species.
- Viewing expression profile for a gene immediately after DE or high expression analysis should select corresponding dataset as default.
Version 4.7.6 (2018-01-04)
- Self-registration temporarily disabled due to email issues.
Version 4.7.5 (2017-05-30)
- Fixed a bug where barplot of expression was showing averages over non-zero values only for each bar.
- Multiple values with zero values at a bar will now be shown scattered next to each other instead of on top of each other.
Version 4.7.4 (2016-10-26)
- Added the "High Expression Search" function on the search page. This can be used to find genes highly expressed in selected sample group.
- Pubmed id has been added to Haemopedia datasets.
Version 4.7.3 (2016-09-02)
- save figure on expression page now uses png instead of pdf, because the code behind png creation is more reliable.
- Reference to published paper has been updated.
Version 4.7.2 (2016-07-21)
- haemopedia page is now publicly accessible, as the manuscript will be published online soon.
- The cause of occasional server crashes has been identified and fixed, so the server should be a lot more stable now.
Version 4.7.1 (2016-06-02)
- Dataset analysis page now shows the same preset colours for sample group items if available, rather than using generic colours.
- Dataset analysis page now shows items in the table in the same order as seen in expression profile graph.
- Barplot colours on the heatmap page now uses the same preset colours for the sample group items if available.
Version 4.7 (2016-05-05)
- Added new datasets "rapin" and "gxcommons".
- Datasets can now be selected so that not all datasets are shown this works like a user preference for a registered user.
- Datasets can now be ordered works as a user preference for a registered user.
- Dataset subsets can now be created from samples page. This subset will be stored under a registered user.
- Improved performance of each page that uses a list of dataset attributes.
Version 4.6.1 (2016-03-03)
- Fixed a bug with dataset download function.
Version 4.6 (2016-02-10)
- Heatmap rendering has now changed: columns are now in the same order as dataset rather than clustered, and z scores are used to cluster and colour rather than expression values.
- Heatmap page has more detailed explanations on how it works.
- haemopedia updated to v2.7 and haemopedia-plus updated to v2.6: updated sample metadata by improving ordering of cell types shown.
Version 4.5 (2016-02-04)
- Updated gene annotation using the latest sources from Ensembl, Entrez and MGI.
- Datasets page now has a version column. This is an internal dataset version used by Haemosphere.
- Datasets page now has the help icon for showing tips.
- dmap dataset updated to v1.2: now has cell lineage and maturity values assigned to each cell type.
- haemopedia updated to v2.6 and haemopedia-plus updated to v2.5: updated some sample data.
Version 4.4 (2015-12-10)
- Downloading the pdf of expression profile plot now uses correct font (sans-serif), however this still does not seem to work on Firefox (works in Chrome).
- Correlation analysis now returns a gene set which is already sorted by correlation value (highest to lowest).
- Differential expression analysis now returns a gene set which is already sorted by logFC.
- Fixed a bug in heatmap where it wasn't correctly selecting the dataset chosen.
- Improved speed of loading each page.
Version 4.3 (2015-12-04)
- Fixed a bug on heatmap page where changing sample group did not change the selector after page refresh.
- Fixed a bug on heatmap page where selecting surface_markers in the sample group caused an error.
- Gene set name truncates after 50 characters (followed by ellipses) if it's too long on the Gene page (hovering will still show the full name).
- R code used by differential expression analysis is available for viewing on Differential Expression Search page.
- haemopedia dataset has been split into haemopedia-plus (contains non-haematopoietic cells) and haemopedia.
Version 4.2 (2015-11-13)
- Added symbols on gene set page for accessing various functions to make them more obvious.
- Exact matching now is possible on the search page.
- Gene set page now has checkboxes for manually selecting individual genes. This can be used to create a new gene set with modified gene list.
Version 4.1 (2015-11-06)
- Fixed a bug where a gene with multiple probes wasn't showing all the probes.
- First version to be accessible by the public. Note that haemopedia is not available at this stage, until manuscript submission.
- Dataset analysis page refreshes without using run button.
- Added favicon.
Version 4.0 (2015-10-20)
- Major release with reconstructed code to get it ready for publication. Many changes have been made from previous version.
- Downloading dataset files can be done faster and without zipping by selecting the type of file needed.
- You can download figures as pdf for print quality.
- Published datasets are now accessible without being a registered user.
- MDS plot has a distance line which is visible when a single point is selected. Use this to see exactly which points are closest.
- Axes labels of MDS plot now correctly reflect selected dimensions.
- Fixed a bug where search by uploading genes didn't work with gene ids properly.
- Gene set page now has a help icon for some tips on using the page and help on hover for most links.
- Gene set page now has Links column to handle all external links such as Ensembl, Entrez, OMIM.
- Keyword search and gene upload has been combined on the search page since they more or less performed the same way.
- About and search pages have improved layout to fit better on narrower browser windows.
- Fixed a bug where heatmap would return internal server error if no expression profile could be found for any of the genes in the dataset.