Supplementary data for the article "funMotifs: Tissue-specific transcription factor motifs"

SND-ID: 2024-343. Version: 1. DOI: https://doi.org/10.57804/y6dd-4f83

Citation

Creator/Principal investigator(s)

Karolina Smolinska - Uppsala University, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics orcid

Husen Muhammad Umer - Uppsala University / Karolinska Institutet, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics / Department of Oncology-Pathology

Nour-al-dain Marzouka - Lund University, Department of Clinical Sciences

Claes Wadelius - Uppsala University, Department of Immunology, Genetics and Pathology orcid

Jan Komorowski - Uppsala University, Department of Cell and Molecular Biology, Computational Biology and Bioinformatics orcid

Research principal

Uppsala University rorId

Description

We built a framework to identify tissue-specific functional motifs (funMotifs) across the genome based on thousands of annotation tracks obtained from large-scale genomics projects including ENCODE, RoadMap Epigenomics and FANTOM. The annotations were weighted using a logistic regression model trained on regulatory elements obtained from massively parallel reporter assays. Overall, genome-wide predicted motifs of 519 TFs were characterized across fifteen tissue types. funMotifs summarizes the weighted annotations into a functional activity score for each of the predicted motifs.

Please read the article the data contributed to for further information: https://doi.org/10.1101/683722.

The dataset was originally published in DiVA and moved to SND in 2024.

Data contains personal data

No

Language

Method and outcome

Data format / data structure

Data collection
Geographic coverage
Administrative information

Contributor(s)

Zeeshan Khaliq - Uppsala university, Science for Life Laboratory, SciLifeLab

Identifiers

Topic and keywords

Research area

Bioinformatics (computational biology) (Standard för svensk indelning av forskningsämnen 2011)

Publications

Husen M. Umer, Karolina Smolinska-Garbulowska, Nour-al-dain Marzouka, Zeeshan Khaliq, Claes Wadelius, Jan Komorowski
bioRxiv 683722; doi: https://doi.org/10.1101/683722
DOI: https://doi.org/10.1101/683722

If you have published anything based on these data, please notify us with a reference to your publication(s). If you are responsible for the catalogue entry, you can update the metadata/data description in DORIS.

Published: 2021-10-11
Last updated: 2024-08-21