| Current release ► | MethMotif version 2.1 |
Program updates:
We have added a search bar to the top of methmotif.org/heatmap/. This facilitates easier access to the transcription factor of interest. By clicking search the TF is highlighted in orange on the heatmap. |
12 June 2023 |
| MethMotif version 2.1 |
Program updates:
Updates were made to the Motif Database: 1) Added pioneer factor information from our meta analysis; 2) Known pioneer factors are denoted with a "*"; 3) The TF Card of known pioneer factors contains the published evidence for the designation as well as references. ex CEBPB |
17 May 2023 | |
| MethMotif version 2.1 |
Bug fixed:
Fixed the issue with redirection when using the header navbar throughout methmotif.org. |
12 May 2023 | |
| MethMotif version 2.1 |
Program updates:
Hover function was replace with a click for: 1) The Motif location; 2) The Cofactor Report. |
19 April 2023 | |
| MethMotif version 2.1 |
Program updates:
Updates were made to the TF card: 1) The Forked logo display; 2) The legend within the Forked Logo display and download. |
6 April 2023 | |
| MethMotif version 2.1 |
Bug fixed:
Fixed the glitch in FPWM Matrix visualization at methmotif.org/motif_display/. |
14 March 2023 | |
| MethMotif version 2.1 |
Bug fixed:
Fixed the bug found on the TF Card at methmotif.org/motif_display/ where the Forked Logo download was in the wrong format. |
10 March 2023 | |
| MethMotif version 2.1 |
Program updates:
A local version of the MethMotif database is now available at methmotif.org/API_TFregulomeR/downloads/. This can be downloaded in order to increase the efficiency of TFregulomeR. |
1 March 2023 | |
| 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 |
| 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 |
| 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 |
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