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Article: BloodChIP Xtra: an expanded database of comparative genome-wide transcription factor binding and gene-expression profiles in healthy human stem/progenitor subsets and leukemic cells

TitleBloodChIP Xtra: an expanded database of comparative genome-wide transcription factor binding and gene-expression profiles in healthy human stem/progenitor subsets and leukemic cells
Authors
Issue Date5-Jan-2024
PublisherOxford University Press
Citation
Nucleic Acids Research, 2024, v. 52, n. D1, p. D1131-D1137 How to Cite?
AbstractThe BloodChIP Xtra database (http://bloodchipXtra.vafaeelab.com/) facilitates genome-wide exploration and visualization of transcription factor (TF) occupancy and chromatin configuration in rare primary human hematopoietic stem (HSC-MPP) and progenitor (CMP, GMP, MEP) cells and acute myeloid leukemia (AML) cell lines (KG-1, ME-1, Kasumi1, TSU-1621-MT), along with chromatin accessibility and gene expression data from these and primary patient AMLs. BloodChIP Xtra features significantly more datasets than our earlier database BloodChIP (two primary cell types and two cell lines). Improved methodologies for determining TF occupancy and chromatin accessibility have led to increased availability of data for rare primary cell types across the spectrum of healthy and AML hematopoiesis. However, there is a continuing need for these data to be integrated in an easily accessible manner for gene-based queries and use in downstream applications. Here, we provide a user-friendly database based around genome-wide binding profiles of key hematopoietic TFs and histone marks in healthy stem/progenitor cell types. These are compared with binding profiles and chromatin accessibility derived from primary and cell line AML and integrated with expression data from corresponding cell types. All queries can be exported to construct TF–gene and protein–protein networks and evaluate the association of genes with specific cellular processes.
Persistent Identifierhttp://hdl.handle.net/10722/348621
ISSN
2023 Impact Factor: 16.6
2023 SCImago Journal Rankings: 7.048

 

DC FieldValueLanguage
dc.contributor.authorThoms, Julie A.I.-
dc.contributor.authorKoch, Forrest C.-
dc.contributor.authorRaei, Alireza-
dc.contributor.authorSubramanian, Shruthi-
dc.contributor.authorWong, Jason W.H.-
dc.contributor.authorVafaee, Fatemeh-
dc.contributor.authorPimanda, John E.-
dc.date.accessioned2024-10-11T00:30:53Z-
dc.date.available2024-10-11T00:30:53Z-
dc.date.issued2024-01-05-
dc.identifier.citationNucleic Acids Research, 2024, v. 52, n. D1, p. D1131-D1137-
dc.identifier.issn0305-1048-
dc.identifier.urihttp://hdl.handle.net/10722/348621-
dc.description.abstractThe BloodChIP Xtra database (http://bloodchipXtra.vafaeelab.com/) facilitates genome-wide exploration and visualization of transcription factor (TF) occupancy and chromatin configuration in rare primary human hematopoietic stem (HSC-MPP) and progenitor (CMP, GMP, MEP) cells and acute myeloid leukemia (AML) cell lines (KG-1, ME-1, Kasumi1, TSU-1621-MT), along with chromatin accessibility and gene expression data from these and primary patient AMLs. BloodChIP Xtra features significantly more datasets than our earlier database BloodChIP (two primary cell types and two cell lines). Improved methodologies for determining TF occupancy and chromatin accessibility have led to increased availability of data for rare primary cell types across the spectrum of healthy and AML hematopoiesis. However, there is a continuing need for these data to be integrated in an easily accessible manner for gene-based queries and use in downstream applications. Here, we provide a user-friendly database based around genome-wide binding profiles of key hematopoietic TFs and histone marks in healthy stem/progenitor cell types. These are compared with binding profiles and chromatin accessibility derived from primary and cell line AML and integrated with expression data from corresponding cell types. All queries can be exported to construct TF–gene and protein–protein networks and evaluate the association of genes with specific cellular processes.-
dc.languageeng-
dc.publisherOxford University Press-
dc.relation.ispartofNucleic Acids Research-
dc.rightsThis work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.-
dc.titleBloodChIP Xtra: an expanded database of comparative genome-wide transcription factor binding and gene-expression profiles in healthy human stem/progenitor subsets and leukemic cells -
dc.typeArticle-
dc.description.naturepublished_or_final_version-
dc.identifier.doi10.1093/nar/gkad918-
dc.identifier.pmid37870453-
dc.identifier.scopuseid_2-s2.0-85181760513-
dc.identifier.volume52-
dc.identifier.issueD1-
dc.identifier.spageD1131-
dc.identifier.epageD1137-
dc.identifier.eissn1362-4962-
dc.identifier.issnl0305-1048-

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