New datasets for C. elegans, S. cerevisiae, S. pombe and A thaliana
The MGA database has several new data sets:
PWMScan: Speeding up the scanning process by parallelization
The scanning task has been sped up by distributing the application on several processing units.
PWMTrain: new sequence library from SMiLE-seq (Isakova et al., 2017)
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.
ChIP-Extract tool: new heatmap row ordering based on k-means Clustering
The rows of the heatmap generated by ChIP-Extract can now be ordered using three methods:
New release of D. melanogaster EPDnew database (v. 005)
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.
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:
Adding support for the H. sapiens Dec 2013 GRCh38/hg38 genome assembly.
The MGA database includes 5 new data sets for the Human genome assembly GRCh38/hg38:
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.
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.
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:
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.
New datasets for A. thaliana
Four new datasets for A. thaliana (Feb 2011 TAIR10/araTha1) have been added to the MGA database.
New dataset for A. thaliana
One new dataset for A. thaliana (Feb 2011 TAIR10/araTha1) has been added to the MGA database.
New dataset for H. sapiens
One new dataset for H. sapiens (Feb 2009 GRCh37/hg19 assembly) has been added to the MGA database.
"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.
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.
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.
OPROF/CPR: new Sequence Shuffling feature
Run the programs for both real and shuffled sequences and produce composite plots.
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.
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.
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.
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.
New release for EPDnew D. melanogaster (v. 003)
New publication describing the ChIP-Seq tools
New publication describing the ChIP-Seq tools
New publication describing the ChIP-Seq tools
New publication describing the ChIP-Seq tools
New release for EPDnew A. thaliana (v. 002)
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.
New release for EPDnew S. cerevisiae (v. 002)
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.
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.
Release of EPD version 128
Automatic release of EPD based on EMBL 128. The user manual for this version can be read here
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.
Release of EPD version 127
Automatic release of EPD based on EMBL 127. The user manual for this version can be read here.
New dataset for hg19 (andersson14): H3K4me1 and H3K27ac in several blood cell types.
New dataset for mm9 (koch11): Maps of pre-initiation complex components in T-cells.
New dataset for dm3 (weber14): Nucleosomes, H2A.Z and RNA in S2-DRSC knockdown cells.
New dataset for hg19 (McCabe12): Analysis of H3K27me3 in EZH2 mutant and wild type DLBCL cell lines
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.
First release of EPDnew for S. pombe
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.
Release of EPD version 125
Automatic release of EPD based on EMBL 125. The user manual for this version can be read here.
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.
New ChIP-seq dataset for hg19 (Zwart 2013): ERα ChIP-seq from breast cancer biopsies
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.
First release of EPDnew for S. cerevisiae
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.
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.
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.
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.
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.
Additional TSS annotation for S. cerevisie
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..
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++.
New implementation of the matrix_scan program (PWMScan)
The matrix_scan algorithm has been implemented in C, resulting in a more efficient program.
Release of EPD version 124
Automatic release of EPD based on EMBL 124. The user manual for this version can be read here.
|10-12-2014||EPD||Released EPDnew collection version 001 for A. thaliana (thale cress) annotated on TAIR10/araTha1 genome|
|21-08-2014||EPD||Released EPDnew collection version 001 for C. elegans (worm) annotated on ce6 genome|
|16-06-2014||EPD||Released new web-site|
|16-06-2014||EPD||Released EPDnew collection version 003 for Homo sapiens (human) annotated on hg19 genome|
|16-06-2014||EPD||Released EPDnew collection version 002 for Drosophila melanogaste (Fruitfly) annotated on dm3 genome|
|23-05-2014||EPD||Released EPDnew collection version 002 for Mus musculus (mouse) annotated on mm9 genome|
|18-09-2013||EPD||Released EPDnew collection version 001 for Danio rerio (zebrafish) annotated on Zv9/danRer7 genome|
|06-02-2013||EPD||Released EPDnew collection version 002 for Homo sapiens annotated on hg19 genome|
|26-09-2012||EPD||Released EPDnew collection version 001 for Drosophila melanogaster|
|09-03-2012||EPD||Released ENSEMBL66 promoter database for Drosophila melanogaster|
|02-03-2012||EPD||Released ENSEMBL66 promoter database for human|
|01-03-2012||EPD||New web-site design implemented|
|15-02-2012||EPD||EPDnew mouse created version 000|
|05-02-2012||EPD||Added ENSEMBL65 for human and mouse collections|
|01-02-2012||EPD||EPDnew human upgraded to version 001|