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

• Published in: Nucleic acids research Vol. 52; no. D1; pp. D1131 - D1137
• Main Authors: Thoms, Julie A I, Koch, Forrest C, Raei, Alireza, Subramanian, Shruthi, Wong, Jason W H, Vafaee, Fatemeh, Pimanda, John E
• Format: Journal Article
• Language: English
• Published: England Oxford University Press 05.01.2024
• ISSN: 0305-1048; 1362-4962
• DOI: 10.1093/nar/gkad918

Abstract The 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. Graphical Abstract Graphical Abstract