News archives

We are in the process of moving the EPD server to the SIB Swiss Institute of Bioinformatics. The new server is up and ready for use. Final tests are underway. We encourage our users to switch to the new server as of now. The current URL https://epd.epfl.ch will soon be automatically redirected.

This manuscript, which includes technical information as well as detailed presentions of several interesting use cases, is available at

https://doi.org/10.1101/2022.05.01.490187.

Happy reading!

We are very pleased to announce the first release of new UCSC-based visualization platform for cancer-related epigenetic data for the human genome assembly hg19. More information about the Breast Cancer Hub can be found here.

We are very happy to announce the first release of a non-coding RNA promoter collection for H. sapiens, which encompasses antisense and long intergenic non-coding RNAs. It is based on the HGNC, Ensembl and RefSeq gene annotation, and it uses TSS mapping data from both the ENCODE and FANTOM5 consortia. More information about the protocol used to build this collection can be found here, and about its quality here.

The following new data sets have been added to the MGA database:

• H. sapiens
• Stelloo 2018, ChIP-seq against AR, H3K27ac, H3K4me3 and H3K27me3 in prostate cancer primary tumors
• EPDnewNC, EPDnew for non-coding (NC) RNAs
• HGNC, TSS collection
• G. gallus
• Schmidt 2010, Mapping of HNF4a and CEBPA in liver

Various histone marks for H. sapiens (hg19 and hg38), chicken (G. gallus) and baking yeast (S. cerevisiae) can now be viewed at the UCSC genome browser. Click on the links to see examples!

Nucleosome maps for zebrafish (D. rerio), thale cress (A. thaliana), fission yeast (S. pombe) and roundworm (C. elegans) can now be viewed at the UCSC genome browser. Click on the links to see examples!

We provide support for the P. falciparum 3D7 genome at EPD (FTP site here) as well as at the ChIP-Seq and SSA Web tools. Transcript mapping data can be visualized at single-base resolution via the public "EPD viewer hub" at the UCSC genome browser.

Collection of regulatory regions in human deriving from a large-scale integrative analysis of ChIP-seq experiments for hundreds of transcriptional regulators (TRs) such as transcription factors, transcriptional co-activators and chromatin regulators. The ReMap 2018 collection comprises a total of 2829 ChIP-seq datasets covering a total of 485 TRs with a catalog of 80M peaks. More information about data samples and processing can be found on the doc page.

ChIP-seq of ER-α, PR, p300 in two ER+ breast cancer cell lines (MCF7 and T47D), and in xenografted MCF7 tumors grown in mice. More information about data samples and processing can be found on the doc page.

We provide support for the G. gallus and C. familiaris genomes at EPD as well as at the ChIP-Seq and SSA Web tools. Compared to the corresponding ENSEMBL gene catalogs, the EPD promoter collections are of higher quality with improved distribution of core promoter elements in the expected positions.

The new software release includes the following updates:

• New C program pwm_scoring to score FASTA-formatted sequences with either an integer PWM or a base probability matrix;
• New bash scripts: pwm_scan_ucsc and pwm_mscan_wrapper_ucsc to deal with chromosome files downloaded from UCSC;
• New bash script pwmlib_scan_seq to scan a sequence with a PWM collection.

The new software release includes the following updates:

• Replace format conversion Perl scripts sga2bed.pl, sga2wig.pl, and bed2sga.pl with corresponding C programs (sga2bed, sga2wig, bed2sga);
• Add format conversion program bed2bed_display to convert BED to BED track suitable for visualizing signal peak regions;
• chippeak: add check on chromosome boundaries after peak refinement;
• chipcenter: add check on chromosome boundaries after read shifting;
• Update User's Guide.

PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix., Bioinformatics, 2018 (DOI: 10.3410/f.732809456.793548094), has been recommended in F1000Prime as being of special significance in its field by F1000 Faculty Member Wyeth W Wasserman. You can read Dr Wasserman’s recommendation here.

We are constantly trying to make EPD and the EPD web-site better. To achieve this we need your help by taking our short survey on how you use EPD and what you would like to see in term of tools and organisms covered. Please follow this link to access it.

With this release we start the support of R. norvegicus genome on EPD and its sisters tools (ChIP-Seq and SSA). Compared to ENSEMBL92 gene catalog, this promoter collection is of higher quality with much better distribution of core promoter elements in the expected positions.

We are pleased to announce the release of the newest mouse (M. musculus v003) promoter collection derived from the latest UCSC genes database and FANTOM5 data (965 samples). The data is mapped to GRCm38/mm10 genome assembly. Collection information and statistics can be found in the mouse EPDnew homepage

We are pleased to announce the release of a new promoter database for A. thaliana. It uses data from 4 different published papers totalling 13 samples on different conditions and tissues.

To prevent a large proportion of zero-value scores, the letter-probability matrix can be re-normalized using an ad hoc pseudo-weight.

We are very happy to announce the release of a new promoter collection for S. pombe (v. 002). We used many more samples to validate promoters (16 compared to 1 for the previous release) and added 5-utr peaks in the processing pipeline. This has brought the coverage to more than 90% of annotated genes!. More information about the protocol used to build this collection can be found here, and about its quality here.

We are very happy to announce the release of a new promoter collection for H. sapiens (v. 006). It is our first release that uses RAMPAGE data (paired-end TSS mapping) and is base on the latest Gencode gene annotation. It also uses data from both the ENCODE and FANTOM5 consortia. More information about the protocol used to build this collection can be found here, and about its quality here.

ChIPseq of MLL3, FOXA1, GRHL2, H3K4me3, H3K4me1 in asynchronous MCF7 cells. More information about samples data processing can be found on the doc page.

The following new data sets have been added to the MGA database:

• H. sapiens
• Schmidt 2012, CTCF binding evolution in mammals.
• M musculus
• Schmidt 2012, CTCF binding evolution in mammals.
• D. melanogaster
• Davie 15, ATAC and FAIRE-seq for the discovery of regulatory regions driving tumor development.
• D. rerio
• Perezrico17, H3K27ac maps in several adult tissues.

Two new data sets have been added to the MGA database:

• H. sapiens
• Buenrostro 2013, ATAC-seq profiling of open chromatin, DNA-binding proteins and nucleosome position.
• M musculus
• Maatouk 2017, Genome-wide identification of regulatory elements in Sertoli cells.

A new article describing the PWMScan Web server and source code has been published in Bioinformatics:

• Ambrosini G. et al., PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
  Bioinformatics, bty127

A new article describing the PWMScan Web server and source code has been published in Bioinformatics:

• Ambrosini G. et al., PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
  Bioinformatics, bty127

A new article describing the PWMScan Web server and source code has been published in Bioinformatics:

• Ambrosini G. et al., PWMScan: a fast tool for scanning entire genomes with a position-specific weight matrix
  Bioinformatics, bty127

The peak files from the following data sets belonging to the ENCODE project have been processed again in order to include the "signalValue" measurement that is used to score the peaks:

• GSE31363, Transcription Factor Binding Sites by Epitope-Tag ChIP-seq from ENCODE/University of Chicago
• Wang et al. 2012, Transcription Factor Binding Sites from ENCODE/Stanford/Yale/USC/Harvard
• Wang et al. 2012, CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington

The peak files from the following data sets belonging to the ENCODE project have been processed again in order to include the "signalValue" measurement that is used to score the peaks:

• GSE31363, Transcription Factor Binding Sites by Epitope-Tag ChIP-seq from ENCODE/University of Chicago
• Wang et al. 2012, Transcription Factor Binding Sites from ENCODE/Stanford/Yale/USC/Harvard
• Wang et al. 2012, CTCF Binding Sites by ChIP-seq from ENCODE/University of Washington

The software for running PWMScan in command-line mode is available on SourceForge at: https://sourceforge.net/projects/pwmscan

Users can provide their own genomic regions (BED files or FASTA files) where to perform transcription factor binding site (TFBS) predictions. The BED-restricted background composition is automatically computed by the back-end software. Alternatively, users can provide their own background composition in the designated text box in the left side input form ("Bg base composition").

The genome-wide motif matches identified by PWMScan are intersected, using the intersect tool of the BEDTools toolset, with BED-defined genomic regions that users can upload to the PWMScan Web site. In addition, users have the possibility to upload sequence sets in FASTA format so as to limit the scanning process to user-defined nucleotide sequences.

The JASPAR CORE motif database has been updated to version JASPAR 2018, and the HOCOMOCO collection to version 11. Two new motif databases have been added to the PWMTools and SSA Web servers: - SMiLE-seq (for human, mouse, and fruit fly) - CIS-BP, a large Catalog of Inferred Sequence Binding Preferences, which includes more than 42

Partial support for the genome assembly Xenopus laevis (NCBI version: Xenopus_laevis_v2, and UCSC assembly name: xenLae2) has been added to the ChIP-Seq and SSA tools.

The genome assembly Xenopus laevis (NCBI version: Xenopus_laevis_v2, and UCSC assembly name: xenLae2) has been added to the PWMScan tool. Partial support for this genome assembly is provided by the ChIP-Seq and SSA Web servers.

The MGA database has several new data sets:

• C. elegans
• Albritton 2017, The genetic mechanisms that allow dosage compensation of the X chromosomes
• Kranz13, Genome-wide analysis of condensin binding
• S. cerevisiae
• Kuang 2014, high-resolution view of chromatin states across distinct metabolic states.
• Sadeh 2016, Combinatorial Chromatin States at Single-Nucleosome Resolution.
• S. pombe
• Lee 2017, Histone H3, Pol2 and various chromatin remodelers in wild type and mutant S. pombe strains
• Jih 2017, mechanisms of heterochromatin assembly
• GSE99589, The Ino80 complex mediates epigenetic centromere propagation via active removal of histone H3
• A. thaliana
• omalley16, A Comprehensive Atlas of Arabidopsis Regulatory DNA [DAP-seq]

The scanning task has been sped up by distributing the application on several processing units.

SMiLE-seq is a new technique for the characterization of DNA-binding proteins in a much faster, more accurate and efficient way. We added sequence data from Isakova et al., 2017 that includes 58 full-length human, mouse, and fruit fly transcription factors (TFs) from distinct structural classes.

The rows of the heatmap generated by ChIP-Extract can now be ordered using three methods:

• ordering based on the Resemblance to the Average Signal Pattern;
• ordering by Center of Gravity from Left to Right;
• ordering based on the k-means Clustering Algorithm.

We are please to announce the release of a new promoter database for D. melanogaster. This release was generated using the recently published data from Schor et al., 2017 along data used in the previous versions. As usual, the quality of the release can be checked in the D. melanogaster database homepage and the procedure used to generate it in the documentation page.

A new Web page is available to full-text search our local collection of publicly available datasets, and easily navigate through our analysis tools:

• MGA-Search

The MGA database includes 5 new data sets for the Human genome assembly GRCh38/hg38:

• FANTOM5: A promoter-level mammalian expression atlas
• GSE34448: CAGE data from several cell lines and locations
• ENSEMBL69 TSS Collection
• EPDnew: the Human Curated Promoter Database
• GENCODE TSSs for known genes

16 new datasets (8 for H.sapiens Feb 2009 GRCh37/hg19, 6 for M.musculus July 2007 NCBI37/mm9 and 2 for D.melanogaster Aug 2014 BDGP Rel6 + ISO1 MT/dm6 ) have been added to the MGA database.

• Human HOCOMOCOv9-00001: List of motif matches from HOCOMOCOv9 with p-value of 10e-4
• Human HOCOMOCOv9-000001: List of motif matches from HOCOMOCOv9 with p-value of 10e-5
• Human HOCOMOCOv10-00001: List of motif matches from HOCOMOCOv10 with p-value of 10e-4
• Human HOCOMOCOv10-000001: List of motif matches from HOCOMOCOv10 with p-value of 10e-5
• Human JasparCore2014-00001: List of motif matches from JasparCore vertebrates 2014 with p-value of 10e-4
• Human JasparCore2014-000001: List of motif matches from JasparCore vertebrates 2014 with p-value of 10e-5
• Human JasparCore2016-00001: List of motif matches from JasparCore vertebrates 2016 with p-value of 10e-4
• Human JasparCore2016-000001: List of motif matches from JasparCore vertebrates 2016 with p-value of 10e-5
• Mouse HOCOMOCOv10-00001: List of motif matches from HOCOMOCOv10 with p-value of 10e-4
• Mouse HOCOMOCOv10-000001: List of motif matches from HOCOMOCOv10 with p-value of 10e-5
• Mouse JasparCore2014-00001: List of motif matches from JasparCore vertebrates 2014 with p-value of 10e-4
• Mouse JasparCore2014-000001: List of motif matches from JasparCore vertebrates 2014 with p-value of 10e-5
• Mouse JasparCore2016-00001: List of motif matches from JasparCore vertebrates 2016 with p-value of 10e-4
• Mouse JasparCore2016-000001: List of motif matches from JasparCore vertebrates 2016 with p-value of 10e-5
• Drosophila OnTheFly2014-00001: List of motif matches from OnTheFly 2014 with p-value of 10e-4
• Drosophila OnTheFly2014-000001: List of motif matches from OnTheFly 2014 with p-value of 10e-5

We are very happy to announce the release of a new promoter collection for H. sapiens (v. 005). It is our first release for the latest human assembly (Dec 2013 GRCh38/hg38) based on the Gencode gene annotation. It is our best release so far, validating more promoters and covering more genes than ever before. It uses data from both the ENCODE and FANTOM5 consortia. More information about the protocol used to build this collection can be found here, and about its quality here.

A new Web page is available to full-text search our local collection of publicly available datasets, and navigate through our analysis tools:

• MGA-Search

A new promoter collection for A. thaliana (v. 003) is now available. With this version the number of promoters has increased more that 50% covering more that 77% of annotated genes. Data is from 3 publications: Morton et al., 2014, Cumbie et al. 2015 and Tokizawa et al. 2017. More information about the protocol used to build this collection can be found here, and here about its quality.

Four new datasets for A. thaliana (Feb 2011 TAIR10/araTha1) have been added to the MGA database.

• ArabidopsisDAPv1-00001: List of motif matches from ArabidopsisDAPv1 with p-value of 10e-4
• ArabidopsisDAPv1-000001: List of motif matches from ArabidopsisDAPv1 with p-value of 10e-5
• JasparCore2016Plants-00001: List of motif matches from JASPAR CORE 2016 plants with p-value of 10e-4
• JasparCore2016Plants-000001: List of motif matches from JASPAR CORE 2016 plants with p-value of 10e-5

One new dataset for A. thaliana (Feb 2011 TAIR10/araTha1) has been added to the MGA database.

• Song 2016: ChIP-seq of abscisic acid-reponsive transcription factors

One new dataset for H. sapiens (Feb 2009 GRCh37/hg19 assembly) has been added to the MGA database.

• Imbeault 2017: KRAB-ZFP ChIP-seq

We have greatly increased the motif search capabilities around promoters. The "Search Motif" tool has been upgraded with more motif libraries (JASPAR 2016, UniPROBE, SwissRegulon) and many more motifs. Moreover, users can now extend the search to a wider promoter region (up to 5 KB upstream and 1 KB downstream the TSS) and change the cut-off. At the same time we have redesigned the viewer page to make it more easy to read. Have a look at the new page for the MAPK1 promoter.

We have updated the "Select / Download" tool with additional selection choices. It now possible to select promoters using several different IDs (EPDnew ID, ENSEMBL, RefSeq, AGI, etc.) and to restrict the selection to the most representative promoter for a gene. The ID selection was previously done by the "Standard Search" tool. To avoid overlaps, the "Standard Search" will be dropped in a month.

The order of the heatmap rows is re-calculated based on three different criteria: i) resemblance to the average signal pattern, ii) center of gravity of signal counts from left to right, iii) k-means clustering.

Run the programs for both real and shuffled sequences and produce composite plots.

ChIP-Track is a tool that can be used to create wiggle custom tracks for data visualization through the UCSC Genome Browser.

Five new data-sets for H. sapiens (Feb 2009 GRCh37/hg19 assembly) have just been added to the MGA database.

• soufi12: Yamanaka factors (Oct4, Sox2, Klf4 and c-Myc) ChIP-seq in reprogrammed fibroblasts.
• kelly12: Nucleosome mapping in fibroblasts
• yardimci14: DNase-seq of naked DNA from K562 and MCF7 cell lines
• starick15: Glucocorticoid receptor ChIP-exo and ChIP-seq in IMR90, U2OS osteosarcoma and K562 cell lines
• duttke15: 5-GRO-seq and GRO-seq in HelaS3 cells

The viewer pages for A. thaliana, A. mellifera, Z. mays and S. pombe have been updated adding a UCSC-derive picture of the genome context around promoters. Moreover the UCSC Hub containing this data is now publicly available at UCSC.

A new paper describing the latest implementations of EPDnew has been recently published in Nucleic Acid Research (Dreos et al., 2017). It reports the developments of EPDnew database and its expansion on non-vertebrate organisms. Finally, it describes the implementation of a novel tool: ChIP-Extract.

A new promoter collection for D. melanogaster (v. 003) is now available. Data is from 4 publications: Ahsan et al., 2009; Hoskins et al., 2012; Chen et al., 2014; Ni et al., 2010. More information about the protocol used to build this collection can be found here, and about its quality here.

A new paper describing the ChIP-Seq tools and web portal has been published in BMC Genomics: Ambrosini et al., 2016

A new paper describing the ChIP-Seq tools and web portal has been published in BMC Genomics: Ambrosini et al., 2016

A new paper describing the ChIP-Seq tools and web portal has been published in BMC Genomics: Ambrosini et al., 2016

A new paper describing the ChIP-Seq tools and web portal has been published in BMC Genomics: Ambrosini et al., 2016

A new promoter collection for A. thaliana (v. 002) is now available. Data is from two publications: Morton et al., 2014 and Cumbie et al. 2015. More information about the protocol used to build this collection can be found here, and here about its quality.

The liftOver tool has been added to the EPDnew Select / Download page. It is now possible to liftOver several EPDnew collections to other assemblies. To do so, first select promoters in the Select / Download page and then choose the destination assembly option in the output page. The selected promoters will be lifted over to the new assembly and provided in several file formats.

We are very happy to announce the release of a new promoter collection for S. cerevisiae (v. 002). More information about the protocol used to build this collection can be found here, and here about its quality.

We are very happy to announce the release of a new promoter collection for H. sapiens (v. 004). It is our best release so far, using data from both the ENCODE and FANTOM5 consortia. In total there are more than 1000 samples that validate this collection! As a result it has the highest coverage and precision that we ever reach for EPDnew H. sapiens. More information about the protocol used to build this collection can be found here, and here about its quality.

We are happy to announce the first release of a promoter collection for Apis mellifera (Honey Bee). More information about the quality of this collection can be found here.

Automatic release of EPD based on EMBL 128. The user manual for this version can be read here

We are happy to announce the first release of a promoter collection for the important crop Zea mays (corn). This is our first collection for a monocots! With this collection we made an important change in how promoters are ordered: transcription start sites that belong to the same gene are ordered according to their global expression level and not according to their position relative to each other. Here primary TSSs (marked with a _1 at the end of their ID) have always the highest expression levels and are followed by all the other in decreasing order of expression. More information about the quality of this collection can be found here.

Automatic release of EPD based on EMBL 127. The user manual for this version can be read here.

H3K4me1 and H3K27ac maps for a number of major human blood cell types (CD4, CD8, CD19 and CD56). Data is from Andersson et al., 2014. More information about this serie can be found here

Map of pre-initiation complex (PIC) components in mouse primary T-cells. Data from Koch et al., 2011. More information about the serie can be found here

Nucleosomes and H2A.Z maps in S2-DRSC with two knockdown genes (H2Av and YL1). PolII map at nucleotide resolution is done using a novel technique (3NT, mapping of the 3 end of nascent transcripts). Data from Weber et al., 2014, more information can be found here

This serie analyses the H3K27me3 state in 3 diffuse large B-cell lymphoma (DLBCL) cell lines (Pfeiffer, KARPAS-422, WSU-DLCL2) after treatment with an EZH2 inibitor (GSK126). Data is from McCabe et al., 2012, more information can be found here.

This serie is part of the RoadMap consortium. It contains data for the HUES64 cell line (an embryonic stem cell) as it go through differentiation in mesoendoderm, mesoderm, endoderm and ectoderm. Several transcription factors and histone marks were analyzed at each stage of differentiation. Data is from Tsankov et al,. 2015, more information can be found here.

We are happy to announce the release of EPDnew 001 for the model organism S. pombe. More information on the quality of the database can be found here and on data used to generate it here.

To investigate the factors giving raise to a luminal or basal breast tumor subtype, the authors performed several cell fusions between luminal and basal-like cell lines. Fusions yielding viable and stable hybrids were then cultured and used for ChIP-seq assays against H3K27me3 and H3K27Ac. Data are from Su et al, 2015, more information can be found in the corresponding doc page.

Automatic release of EPD based on EMBL 125. The user manual for this version can be read here.

The data in this series have been used to analyze the epigenome of human mammary epithelial cells (HMEC) and a matched variant cell population (vHMEC) that have spontaneously escaped senescence and undergone partial carcinogenic transformation. Histone marks were assayed using ChIP-seq and DNA methylation using Methylated DNA Binding Domain protein Capture (MBDCap-seq). Data are from Locke et al., 2015, more information can be found in the corresponding doc page.

Thanks to an innovative experimental technique, ERα binding sites have been mapped genome-wide through ChIP-seq from 10'000 breast cancer MCF7 cells and tumour biopsies. Data are from Zwart et al., 2013, more information can be found in the corresponding doc page.

The data include the release of EPDnew 001 for the model organism S. cerevisiae. More information can be found in the corresponding doc page.

We are happy to announce the release of EPDnew 001 for the model organism S. cerevisiae. More information on the quality of the database can be found here and on data used to generate it here

A public AMI (Amazon Machine Image) has been created on AWS cloud with our ChIP-Seq analysis tools. The latest version of all the tools has been installed and configured.

The data serie waszak15 comprises population (47 samples) measurements of transcription factors (PU.1 and RPB2) and histone modifications (H3K27ac, H3K4me1 and H3k4me3) in lymphoblastoid cell lines for a subset of the 1000 Genomes Project CEPH samples. Data is from Waszak et al., 2015, more informations can be found in the corresponding doc page.

A new series of 3 RNA-seq samples for A. thalina has been added to the MGA database with name 'Cumbie 15, Nano-CAGE data of Arabidopsis roots'. This is a novel CAGE technique named Nano-CAGE-XL that promises higher coverage and sensitivity.
Data is from Cumbie et al., 2015, more informations can be found in the corresponding doc page.

Schizosaccharomyces pombe MGA database has been populated with 4 data sets, marking the beginning of support for this organism. The 4 data sets are from a wide range of data types:
- 2 annotation sets from PomBase and RefSeq;
- 1 RNA-seq set (CAGE data) from Li et al., 2015;
- 1 ChIP-seq and MNase-seq set (HIstone variants and modifications, nucleosomes) from DeGennaro et al., 2013.

We are pleased to announce the release of ChIP-Seq 1.5-0. The ChIP-Seq software provides methods for the analysis of ChIP-seq data and other types of mass genome annotation data. The most common analysis tasks include positional correlation analysis, peak detection, and genome segmentation. Several format conversion applications are also included. ChIP-Seq 1.5-0 brings many updates and enhancements, among which the addition of a feature correlation and extraction tool (chipextract) that generates heatmaps in numerical format that can be easily imported by other tools such as the R software for statistical computing. The new software package can be downloaded from sourceforge.

An additional S. cerevisie transcription start site annotation serie has been added to the MGA database, which contains TSS coordinates of protein coding genes derived from the Saccharomyces Genome Database. More information about this serie can be found in the corresponding doc page

Allow upload of SGA and BED formatted files, allow upload via URL, and offer the possibility to specify a genome release. The Drosophila OnTheFly 2014 PWM collection has been added to the server menus..

Most of the back-end software of the Word Analysis tool (MSeq) has been replaced by a faster implementation using C and C++.

The matrix_scan algorithm has been implemented in C, resulting in a more efficient program.

Automatic release of EPD based on EMBL 124. The user manual for this version can be read here.