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MethMotif Updates



Current release ► MethMotif version 2.0 Program updates:
Updated TF cards were added to:
1) MethMotif's Explore heatmaps;
2) MethMotif's Batch Query.
13 May 2022
MethMotif version 2.0 Program updates:
TF cards were updated with a TF cofactor list that
includes:
1) TF logos and binding site methylation profiles in the
context of each TF partners;
2) Genomic locations of the TF of interest in the context
of each TF partners;
3) Gene ontology analyses of TF's targets in the context
of each TF partners.
29 April 2022
MethMotif version 2.0 Program updates:
Modified the framework of methmotif.org to increase
portability and interoperability
8 December 2021
MethMotif version 2.0 Program updates:
Local mirror setup on Memorial Univserities compute cluster
Centre for Health Informatics and Analytics (CHIA) for:
1) Testing future updates;
2) Decreasing TFregulomeR's execution time.
29 October 2021
MethMotif version 2.0 Bug fixed:
Fixed the glitch in the Batch Query's CAPTCHA and query
function on methmotif.org/find_motif_tool/.
9 July 2021
MethMotif version 2.0 Program updates:
1) MethMotif plant database was added;
30 November 2020
MethMotif version 2.0 Data updates:
1) MethMotif plant database was added;
2) 23 new factors in plant species Arabidopsis thaliana
were added.
24 June 2020
MethMotif version 1.3 Program updates:
MethMotif has been additionally hosted in Compute Canada
server via https://methmotif.org.
5 March 2020
MethMotif version 1.3 Program updates:
MethMotif API - TFregulomeR has been launched.
5 November 2019
MethMotif version 1.3 Data updates:
1) 18 new DNA binding proteins in GM12878 cell line
were added (details).
2) 2 new DNA binding proteins in H1-hESC cell line
were added (details).
3) 3 new DNA binding proteins in HCT116 cell line
were added (details).
4) 4 new DNA binding proteins in HEK293T cell line
were added (details).
5) 9 new DNA binding proteins in HeLa-S3 cell line
were added (details).
6) 89 new DNA binding proteins in HepG2 cell line
were added (details).
7) 39 new DNA binding proteins in K562 cell line
were added (details).
8) 25 new DNA binding proteins in MCF-7 cell line
were added (details).
15 March 2019
MethMotif version 1.3 Data updates:
1) 16 new DNA binding proteins in LNCaP, a prostate
adenocarcinoma cell line, were added (details).
6 March 2019
MethMotif version 1.3 Data updates:
1) 13 new DNA binding proteins in HEK293 cell line
were added (details).
2) 9 new DNA binding proteins in H9 cell line
were added (details).
3) 18 new DNA binding proteins in HUES64 cell line
were added (details).
2 January 2019
MethMotif version 1.3 Data updates:
17 new DNA binding proteins in HEK293T cell line
were added (details).
28 November 2018
MethMotif version 1.3 Bug fixed:
Malfunction of search engine autocompletion in
https has been fixed.
17 November 2018
MethMotif version 1.3 Data updates:
2 new factors were added in human SNU398 cell line
(details).
6 November 2018
MethMotif version 1.3 Data updates:
1) MethMotif mouse database was added;
2) 39 new factors in mouse MEL cell line were added
(details).
4 November 2018
MethMotif version 1.2 Program updates:
CAPTCHA was added in MethMotif Batch Query to
avoid overloading by robots.
22 October 2018
MethMotif version 1.2 Program updates:
1) A link to MethMotif card was added in MethMotif
Batch Query outputs;
2) Three states of MethMotif logo based on DNA
methylation levels were added;
3) A more explicit MethMotif logo legend was added;
4) Motif distrubition was added for each TFBS.
1 October 2018
MethMotif version 1.1 Data updates:
1) 11 new factors were added for GM12878;
2) 22 new factors were added for MCF-7;
3) 1 new factors were added for H1-hESC;
4) 2 new factors were added for HCT116;
5) No new release for HeLa-S3 in ENCODE.
19 April 2018
MethMotif version 1.1 Data updates:
32 new factors were added for HepG2.
13 April 2018
MethMotif version 1.1 Data updates:
65 new factors were added for K562.
9 April 2018
MethMotif version 1.1 Data updates:
Data for IMR-90, SK-N-SH and A549 were added.
3 April 2018
MethMotif version 1.1 Data updates:
Data for K562, GM12878, HepG2, H1-hESC, MCF-7,
HCT116, HeLa-S3 and HEK293 were added.
26 March 2018



ChIP-seq datasets in MethMotif

Cell ID Organism Cell type/tissue Number of ChIP-seq experiments Source Download date
IMR-90 Human Lung 15 ENCODE 26 Mar 2018
SK-N-SH Human Brain 30 ENCODE 26 Mar 2018
A549 Human Lung 42 ENCODE 26 Mar 2018
SNU398 Human Liver 2 GSE112729, GSE103048 16 Apr 2018
HEK293 Human Kidney 212 ENCODE 10 Dec 2018
H9 Human Stem cell 9 GTRD 11 Dec 2018
HUES64 Human Stem cell 13 GTRD 11 Dec 2018
LNCaP Human Prostate 16 GTRD 11 Dec 2018
GM12878 Human Blood 161 ENCODE/GTRD 11 Dec 2018
H1-hESC Human Stem cell 67 ENCODE/GTRD 11 Dec 2018
HCT116 Human Colorectum 25 ENCODE/GTRD 11 Dec 2018
HEK293T Human Kidney 21 ENCODE/GTRD 11 Dec 2018
HeLa-S3 Human Cervix 66 ENCODE/GTRD 11 Dec 2017
HepG2 Human Liver 227 ENCODE/GTRD 11 Dec 2018
K562 Human Blood 318 ENCODE/GTRD 11 Dec 2018
MCF-7 Human Breast 124 ENCODE/GTRD 11 Dec 2018

Whole genome bisulfite sequencing datasets in MethMotif

Cell ID Organism Cell type/tissue Replicate number Source Release date
HeLa-S3 Human Cervix 1 Buck-Koehntop Lab 30 Jan 2017
IMR-90 Human Lung 1 ENCODE 31 Jul 2013
SK-N-SH Human Brain 2 ENCODE 13 Dec 2017
A549 Human Lung 2 ENCODE 4 Dec 2017
K562 Human Blood 2 ENCODE 22 Mar 2016
HepG2 Human Liver 2 ENCODE 13 Oct 2015
GM12878 Human Blood 2 ENCODE 23 Feb 2016
MCF-7 Human Breast 1 Stunnenberg Lab 3 Jul 2014
H1-hESC Human Stem cell 2 ENCODE 13 Oct 2015
HCT116 Human Colorectum 1 Benoukraf Lab 10 Aug 2018
SNU398 Human Liver 1 Tenen Lab To be released
HEK293T Human Kidney 1 Luo Lab 14 Dec 2016
HEK293 Human Kidney 1 Bierne Lab 11 Dec 2015
H9 Human Stem cell 2 ENCODE 31 Jul 2013
HUES64 Human Stem cell 2 ENCODE 31 Jul 2013
LNCaP Human Prostate 1 Stirzaker Lab 17 Mar 2017