SNP2TFBS

News archives

News from the EPD database and the other tools (ChIP-Seq, SSA, PWMTools) and database (MGA) mantained by the CCG group.

13-07-2017PWMTools

New MGA Query Page to easily access the MGA repository and Analysis Tools

A new Web page is available to full-text search our local collection of publicly available datasets, and easily navigate through our analysis tools:
13-07-2017MGA

Adding support for the H. sapiens Dec 2013 GRCh38/hg38 genome assembly.

10-07-2017MGA

New datasets for H. sapiens, M.musculus and D.melanogaster

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.
10-07-2017EPD

New release for EPDnew H. sapiens mapped on hg38 (v. 005)

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.
16-06-2017MGA

New Full-text Search Hub to easily access the MGA database and Analysis Tools

A new Web page is available to full-text search our local collection of publicly available datasets, and navigate through our analysis tools:
13-06-2017EPD

New release for EPDnew A. thaliana (v. 003)

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.
12-06-2017MGA

New datasets for A. thaliana

Four new datasets for A. thaliana (Feb 2011 TAIR10/araTha1) have been added to the MGA database.
19-05-2017MGA

New dataset for A. thaliana

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
09-05-2017MGA

New dataset for H. sapiens

One new dataset for H. sapiens (Feb 2009 GRCh37/hg19 assembly) has been added to the MGA database.
08-05-2017EPD

"Search Motif" tool of the promoter viewer page has been updated

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.
04-05-2017EPD

The "Select / Download" tool has been given a redesign

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.
25-04-2017ChIP-Seq

ChIP-Extract: more Heatmap ordering options

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.
24-04-2017SSA

OPROF/CPR: new Sequence Shuffling feature

Run the programs for both real and shuffled sequences and produce composite plots.
20-03-2017ChIP-Seq

New tool (ChIP-Track) for data visualization at UCSC

ChIP-Track is a tool that can be used to create wiggle custom tracks for data visualization through the UCSC Genome Browser.
17-03-2017MGA

Five new datasets for H. sapiens

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
25-01-2017EPD

Updated viewer page for A. thaliana, A. mellifera, Z. mays and S. pombe.

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.
29-11-2016EPD

New publication describing the latest EPDnew databases

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.
29-11-2016EPD

New release for EPDnew D. melanogaster (v. 003)

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.
22-11-2016SSA

New publication describing the ChIP-Seq tools

A new paper describing the ChIP-Seq tools and web portal has been published in BMC Genomics: Ambrosini et al., 2016
22-11-2016PWMTools

New publication describing the ChIP-Seq tools

A new paper describing the ChIP-Seq tools and web portal has been published in BMC Genomics: Ambrosini et al., 2016
22-11-2016EPD

New publication describing the ChIP-Seq tools

A new paper describing the ChIP-Seq tools and web portal has been published in BMC Genomics: Ambrosini et al., 2016
22-11-2016ChIP-Seq

New publication describing the ChIP-Seq tools

A new paper describing the ChIP-Seq tools and web portal has been published in BMC Genomics: Ambrosini et al., 2016
17-11-2016EPD

New release for EPDnew A. thaliana (v. 002)

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.
10-10-2016EPD

New liftOver option added to "Select / Download" page

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.
12-09-2016EPD

New release for EPDnew S. cerevisiae (v. 002)

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.
07-09-2016EPD

New release for EPDnew H. sapiens (v. 004)

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.
22-07-2016EPD

First release of EPDnew for Apis mellifera

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.
20-07-2016EPD

Release of EPD version 128

Automatic release of EPD based on EMBL 128. The user manual for this version can be read here
13-06-2016EPD

First release of EPDnew for Zea mays

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.
13-04-2016EPD

Release of EPD version 127

Automatic release of EPD based on EMBL 127. The user manual for this version can be read here.
24-03-2016MGA

New dataset for hg19 (andersson14): H3K4me1 and H3K27ac in several blood cell types.

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
24-03-2016MGA

New dataset for mm9 (koch11): Maps of pre-initiation complex components in T-cells.

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
22-03-2016MGA

New dataset for dm3 (weber14): Nucleosomes, H2A.Z and RNA in S2-DRSC knockdown cells.

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
07-01-2016MGA

New dataset for hg19 (McCabe12): Analysis of H3K27me3 in EZH2 mutant and wild type DLBCL cell lines

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.
04-12-2015MGA

New dataset for hg19 (tsankov15): TF binding dynamics during human ES cell differentiation

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.
16-11-2015EPD

First release of EPDnew for S. pombe

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.
16-11-2015MGA

New data set for hg19 (Su 2015): H3K27me3 and H3K27Ac profiles in multiple breast cancer fusions

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.
23-10-2015EPD

Release of EPD version 125

Automatic release of EPD based on EMBL 125. The user manual for this version can be read here.
21-10-2015MGA

New data set for hg19 (Locke 2015 ): Epigenetic remodelling in early breast carcinogenesis

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.
21-10-2015MGA

New ChIP-seq dataset for hg19 (Zwart 2013): ERα ChIP-seq from breast cancer biopsies

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.
21-10-2015MGA

New EPDnew series for S. cerevisiae

The data include the release of EPDnew 001 for the model organism S. cerevisiae. More information can be found in the corresponding doc page.
08-10-2015EPD

First release of EPDnew for S. cerevisiae

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
16-09-2015ChIP-Seq

ChIP-Seq on Amazon Cloud

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.
15-09-2015MGA

New ChIP-seq series for hg19: population measurements of TFs and histone variants

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.
10-09-2015MGA

New A. thaliana CAGE series

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.
25-08-2015MGA

We are beginning the support of S. pombe

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.
24-08-2015ChIP-Seq

Release of ChIP-Seq 1.5-0

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.
19-08-2015MGA

Additional TSS annotation for S. cerevisie

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
15-08-2015SSA

Improvements on the SSA server navigation tools

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..
13-08-2015PWMTools

Improvements on PWMTools

Most of the back-end software of the Word Analysis tool (MSeq) has been replaced by a faster implementation using C and C++.
11-08-2015PWMTools

New implementation of the matrix_scan program (PWMScan)

The matrix_scan algorithm has been implemented in C, resulting in a more efficient program.
13-07-2015EPD

Release of EPD version 124

Automatic release of EPD based on EMBL 124. The user manual for this version can be read here.
10-12-2014EPDReleased EPDnew collection version 001 for A. thaliana (thale cress) annotated on TAIR10/araTha1 genome
21-08-2014EPDReleased EPDnew collection version 001 for C. elegans (worm) annotated on ce6 genome
16-06-2014EPDReleased new web-site
16-06-2014EPDReleased EPDnew collection version 003 for Homo sapiens (human) annotated on hg19 genome
16-06-2014EPDReleased EPDnew collection version 002 for Drosophila melanogaste (Fruitfly) annotated on dm3 genome
23-05-2014EPDReleased EPDnew collection version 002 for Mus musculus (mouse) annotated on mm9 genome
18-09-2013EPDReleased EPDnew collection version 001 for Danio rerio (zebrafish) annotated on Zv9/danRer7 genome
06-02-2013EPDReleased EPDnew collection version 002 for Homo sapiens annotated on hg19 genome
26-09-2012EPDReleased EPDnew collection version 001 for Drosophila melanogaster
09-03-2012EPDReleased ENSEMBL66 promoter database for Drosophila melanogaster
02-03-2012EPDReleased ENSEMBL66 promoter database for human
01-03-2012EPDNew web-site design implemented
15-02-2012EPDEPDnew mouse created version 000
05-02-2012EPDAdded ENSEMBL65 for human and mouse collections
01-02-2012EPDEPDnew human upgraded to version 001
Last update July 2017