@vorontsovie.bsky.social
Reposted
(12/12) Kudos to the Codebook and GRECO-BIT consortium members including @bartdeplancke.bsky.social, see the whole team at ibis.autosome.org/docs/about_us
IBIS Challenge
ibis.autosome.org
November 14, 2024 at 1:04 PM
(12/12) Kudos to the Codebook and GRECO-BIT consortium members including @bartdeplancke.bsky.social, see the whole team at ibis.autosome.org/docs/about_us
Reposted
(11/12) This project is only one of the multiple facets of the larger Codebook initiative, check dx.doi.org/10.1101/2024...
November 14, 2024 at 1:04 PM
(11/12) This project is only one of the multiple facets of the larger Codebook initiative, check dx.doi.org/10.1101/2024...
Reposted
(10/12) Want something more than simple PWMs? Reaching the next level with IBIS: join the online IBIS conference on November 27, more details soon at ibis.autosome.org.
November 14, 2024 at 1:04 PM
(10/12) Want something more than simple PWMs? Reaching the next level with IBIS: join the online IBIS conference on November 27, more details soon at ibis.autosome.org.
Reposted
(9/12) Check the interactive Codebook/GRECO-BIT Motif Explorer (mex.autosome.org), which provides motifs, performance metrics, ranks, logos, top-performing motifs, and structured metadata.
GRECO-BIT/Codebook Motif Explorer
mex.autosome.org
November 14, 2024 at 1:04 PM
(9/12) Check the interactive Codebook/GRECO-BIT Motif Explorer (mex.autosome.org), which provides motifs, performance metrics, ranks, logos, top-performing motifs, and structured metadata.
Reposted
(8/12) With that many PWMs at hand, we also demonstrate that several motifs can be easily combined into a better model with ArChIPelago: regression or Random Forest on top of PWM scans.
November 14, 2024 at 1:04 PM
(8/12) With that many PWMs at hand, we also demonstrate that several motifs can be easily combined into a better model with ArChIPelago: regression or Random Forest on top of PWM scans.
Reposted
(7/12) Comparison of different tools yielded many surprises. On the one hand, underused motif discovery tools such as Dimont excel across different types of experimental data. On the other hand, no single tool or platform is enough to get the most for each TF and each data type.
November 14, 2024 at 1:04 PM
(7/12) Comparison of different tools yielded many surprises. On the one hand, underused motif discovery tools such as Dimont excel across different types of experimental data. On the other hand, no single tool or platform is enough to get the most for each TF and each data type.
Reposted
(6/12) In total, we processed data from 4,237 experiments and generated 219,939 motifs. 164,350 motifs (for 236 TFs) from curated and approved datasets were taken for benchmarking. The motifs and datasets are available at ZENODO zenodo.org/records/1018....
Codebook Motif Explorer Supplementary Dataset
This is the supplementary dataset of the GRECO-BIT/Codebook Motif Explorer (MEX),which is a detailed online catalog of DNA motifs built using a huge collection of experimental data produced by the Cod...
zenodo.org
November 14, 2024 at 1:04 PM
(6/12) In total, we processed data from 4,237 experiments and generated 219,939 motifs. 164,350 motifs (for 236 TFs) from curated and approved datasets were taken for benchmarking. The motifs and datasets are available at ZENODO zenodo.org/records/1018....
Reposted
(5/12) Testing all existing tools is hardly realistic. Focusing on position weight matrices (PWMs), we tested the most popular tools (e.g. MEME, HOMER), less popular yet powerful tools (e.g. ChIPMunk, Dimont), and a few advanced methods still able to yield PWMs (e.g. ExplaiNN, ProBound).
November 14, 2024 at 1:04 PM
(5/12) Testing all existing tools is hardly realistic. Focusing on position weight matrices (PWMs), we tested the most popular tools (e.g. MEME, HOMER), less popular yet powerful tools (e.g. ChIPMunk, Dimont), and a few advanced methods still able to yield PWMs (e.g. ExplaiNN, ProBound).
Reposted
(4/12) We aimed to tackle both problems by running multiple motif discovery software against a large set of newly generated DNA on human TF-DNA interactions from Codebook [https://dx.doi.org/10.1101/2024.11.11.622097].
November 14, 2024 at 1:04 PM
(4/12) We aimed to tackle both problems by running multiple motif discovery software against a large set of newly generated DNA on human TF-DNA interactions from Codebook [https://dx.doi.org/10.1101/2024.11.11.622097].
Reposted
(3/12) There are a multitude of high-throughput methods for assessing the DNA binding specificity of transcription factors. The variety of existing motif discovery tools is even greater. Which one to use?
November 14, 2024 at 1:04 PM
(3/12) There are a multitude of high-throughput methods for assessing the DNA binding specificity of transcription factors. The variety of existing motif discovery tools is even greater. Which one to use?
Reposted
(2/12) The human genome encodes ~1.5 thousand transcription factors (TFs), and hundreds of them still lack "DNA motifs", i.e., compact human- and machine-readable representations of the TF-DNA binding specificity.
November 14, 2024 at 1:04 PM
(2/12) The human genome encodes ~1.5 thousand transcription factors (TFs), and hundreds of them still lack "DNA motifs", i.e., compact human- and machine-readable representations of the TF-DNA binding specificity.
Reposted
(7/7) Kudos to the Codebook and GRECO-BIT consortium members including @halfacrocodile.bsky.social and @bartdeplancke.bsky.social. See the whole team at ibis.autosome.org/docs/about_us
IBIS Challenge
ibis.autosome.org
November 15, 2024 at 6:49 PM
(7/7) Kudos to the Codebook and GRECO-BIT consortium members including @halfacrocodile.bsky.social and @bartdeplancke.bsky.social. See the whole team at ibis.autosome.org/docs/about_us
Reposted
(6/7) 1,421 human TFs now have a characterized DNA-binding specificity, and nearly all 1,638 have been assayed. Analyses in doi.org/10.1101/2024... indicate, however, that many previously characterized TF binding specificities may be inaccurate.
November 15, 2024 at 6:49 PM
(6/7) 1,421 human TFs now have a characterized DNA-binding specificity, and nearly all 1,638 have been assayed. Analyses in doi.org/10.1101/2024... indicate, however, that many previously characterized TF binding specificities may be inaccurate.
Reposted
(5/7) Collectively the uncharacterized TFs bind directly to tens of thousands of conserved sequences, providing biochemical functions for these sites. Intriguingly, many of these sites are in genomic “dark matter”. Explored further in doi.org/10.1101/2024...
November 15, 2024 at 6:49 PM
(5/7) Collectively the uncharacterized TFs bind directly to tens of thousands of conserved sequences, providing biochemical functions for these sites. Intriguingly, many of these sites are in genomic “dark matter”. Explored further in doi.org/10.1101/2024...
Reposted
(4/7) Methods for PWM discovery and benchmarking are explored in detail in an accompanying manuscript: doi.org/10.1101/2024...
November 15, 2024 at 6:49 PM
(4/7) Methods for PWM discovery and benchmarking are explored in detail in an accompanying manuscript: doi.org/10.1101/2024...
Reposted
(3/7) Of the 332 uncharacterized TFs, PWMs were identified for 177, the vast majority of which have unique and previously unseen motifs.
November 15, 2024 at 6:49 PM
(3/7) Of the 332 uncharacterized TFs, PWMs were identified for 177, the vast majority of which have unique and previously unseen motifs.
Reposted
(2/7) We applied five different assays to 332 uncharacterized TFs (i.e., Codebook TFs) and 61 control TFs, including a new assay, GHT-SELEX, described in: doi.org/10.1101/2024...
November 15, 2024 at 6:49 PM
(2/7) We applied five different assays to 332 uncharacterized TFs (i.e., Codebook TFs) and 61 control TFs, including a new assay, GHT-SELEX, described in: doi.org/10.1101/2024...
Reposted
Last but not least: this update became possible thanks to the experimental data & motif analysis performed within the Codebook/GRECO-BIT collaboration, ibis.autosome.org/docs/about_us
IBIS Challenge
ibis.autosome.org
February 17, 2025 at 11:44 AM
Last but not least: this update became possible thanks to the experimental data & motif analysis performed within the Codebook/GRECO-BIT collaboration, ibis.autosome.org/docs/about_us
Reposted
(4/4) Don't hesitate to grab a fresh release from hocomoco.autosome.org and remember that we also provide a fancy online motif scanner, MoLoTool, in all its interactive JS-powered beauty.
February 17, 2025 at 11:38 AM
(4/4) Don't hesitate to grab a fresh release from hocomoco.autosome.org and remember that we also provide a fancy online motif scanner, MoLoTool, in all its interactive JS-powered beauty.
Reposted
(3/4) Also do not forget that HOCOMOCO also provides motifs for orthologous mouse TFs, >800 of those are covered in v13.
February 17, 2025 at 11:38 AM
(3/4) Also do not forget that HOCOMOCO also provides motifs for orthologous mouse TFs, >800 of those are covered in v13.
Reposted
(2/4) v13 covers >1100 of ~1600 human TFs with >1600 primary motifs and subtypes. Since v12 we also provide a reduced non-redundant set of motifs, which are often shared between TFs with similar DBDs.
February 17, 2025 at 11:38 AM
(2/4) v13 covers >1100 of ~1600 human TFs with >1600 primary motifs and subtypes. Since v12 we also provide a reduced non-redundant set of motifs, which are often shared between TFs with similar DBDs.