COBIND analysis results
02 March 2024
About COBIND
COBIND pipeline was build to identify DNA patterns in a set of sequences. The discovered patterns are relative to the provided anchor regions. For example, one can the co-binding patterns relative to the know transcription factor binding sites (TFBSs). The workflow will discover the patterns de novo, summarize them by determining the spacings and orientation.
The code that was used to produce these COBIND results is stored in this repository. COBIND pipeline is also as a tool and can be found in this repository.
What to expect from this page?
This page contains results from high-scale ChIP-seq data analysis with COBIND. We analysed 5,699 datasets of high-confidence TFBSs stored in UniBind 2021 database for 401 unique TFs that collectively are from 7 species: Arabidopsis thaliana, Caenorhabditis elegans, Danio rerio, Drosophila melanogaster, Homo sapiens, Mus musculus and Rattus norvegicus.
Reports about discovered co-binders are provided for each TF (where at least one co-binder was discovered) in different species. Another group of reports report the discovered co-binders summarized over TF families. Conservation summaries are available for all species, except Danio rerio and Rattus norvegicus.
Species-specific results
Arabidopsis thaliana
Conservation summaries from individual TFs analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Conservation summaries from TF families analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Caenorhabditis elegans
Results for TF families
Conservation summaries from individual TFs analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Conservation summaries from TF families analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Danio rerio
Drosophila melanogaster
Conservation summaries from individual TFs analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Conservation summaries from TF families analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Homo sapiens
Results for individual TFs
Results for TF families
Factors_with_multiple_dispersed_zinc_fingers
More_than_3_adjacent_zinc_finger_factors
TALE-type_homeo_domain_factors
Conservation summaries from individual TFs analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Conservation summaries from TF families analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Mus musculus
Results for individual TFs
Results for TF families
Factors_with_multiple_dispersed_zinc_fingers
More_than_3_adjacent_zinc_finger_factors
Responders_to_external_signals_SRFRLM1
TALE-type_homeo_domain_factors
Three-zinc_finger_Kruppel-related_factors
Conservation summaries from individual TFs analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Conservation summaries from TF families analysis
Distribution of conservation p-values for all co-binders
Distribution of conservation p-values for top most conserved
co-binders
Rattus norvegicus
Results for TF families
Interspecies results
Results for individual TFs
Results for TF families
Factors_with_multiple_dispersed_zinc_fingers
More_than_3_adjacent_zinc_finger_factors
Responders_to_external_signals_SRFRLM1
TALE-type_homeo_domain_factors
Three-zinc_finger_Kruppel-related_factors
Protein-protein interaction (PPI) analysis summary
Numbers of co-binders are summarized in the barplot and reflect the number of anchor-co-binder pairs in different species that had significant motif similarity match in motif libraries, which then was found in the protein-protein data with a significant combined score.See summary plot when compared to species-specific motif libraries
See summary plot when compared to full motif library
Species icons sources
Species icons were taken from:
Contact
In case you have any questions related to COBIND results and pipeline, do not hesitate to contact us:
| Name | |
|---|---|
| Ieva Rauluseviciute | ieva.rauluseviciute@ncmm.uio.no |
| Anthony Mathelier | anthony.mathelier@ncmm.uio.no |