Supplementary data for the article "funMotifs: Tissue-specific transcription factor motifs"
type: Dataset
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.
citation: 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
conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
conditions of access: info:eu-repo/semantics/openAccess
contributor: Zeeshan Khaliq
  type: Person
  affiliation: Uppsala university
  family name: Khaliq
  given name: Zeeshan
creative work status: completed
  type: DefinedTerm
  in defined term set: http://publications.europa.eu/resource/authority/dataset-status
  term code: COMPLETED
creator: Karolina Smolinska
creator: Husen Muhammad Umer
  type: Person
  affiliation: Uppsala University / Karolinska Institutet
    type: Organization
    department: Department of Cell and Molecular Biology, Computational Biology and Bioinformatics / Department of Oncology-Pathology
  family name: Umer
  given name: Husen Muhammad
creator: Nour-al-dain Marzouka
  type: Person
  affiliation: Lund University
  family name: Marzouka
  given name: Nour-al-dain
creator: Claes Wadelius
creator: Jan Komorowski
date modified: 2024-08-21
date published: 2021-10-11
language: English
is part of: https://doi.org/10.57804/kgwy-b661
keywords: Bioinformatics (Computational Biology)
  type: DefinedTerm
  term code: 10203
keywords: genomics
keywords: gene expression
publisher: Uppsala university
distribution: data/ATTACHMENT02.pdf
  type: DataDownload
  additional type: data
  conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
  conditions of access: info:eu-repo/semantics/openAccess
  content size: 626630
  encoding format: application/pdf
distribution: data/DATASET01.xlsx
  type: DataDownload
  additional type: data
  conditions of access: http://publications.europa.eu/resource/authority/access-right/PUBLIC
  conditions of access: info:eu-repo/semantics/openAccess
  content size: 1727947
  encoding format: application/vnd.openxmlformats-officedocument.spreadsheetml.sheet
version: 1

PropertyValue
property ID: DOI
value: 10.57804/y6dd-4f83

PropertyValue
property ID: URN
value: urn:nbn:se:uu:diva-455848

PropertyValue
property ID: DOI
value: 10.1101/683722

Uppsala university
type: Organization
department: Science for Life Laboratory, SciLifeLab
name: Uppsala University
department: Department of Cell and Molecular Biology, Computational Biology and Bioinformatics
department: Department of Immunology, Genetics and Pathology

Karolina Smolinska
type: Person
affiliation: Uppsala university
family name: Smolinska
given name: Karolina

Lund University
type: Organization
department: Department of Clinical Sciences

Claes Wadelius
type: Person
affiliation: Uppsala university
family name: Wadelius
given name: Claes

Jan Komorowski
type: Person
affiliation: Uppsala university
family name: Komorowski
given name: Jan

English
type: Language
alternate name: eng

genomics
type: DefinedTerm
term code: p5146

gene expression
type: DefinedTerm
term code: p25831