LymphTF-DB: a database of transcription factors involved in lymphocyte development

B and T cells develop following a similar early stepwise progression to later stages where multiple developmental options are available. These developmental regimes necessitate differential gene expression regulated by a large number of transcription factors (TFs). The resultant burgeoning amount of information has opened a knowledge gap between TF activities during lymphocyte development and a researcher's experiments. We have created the LymphTF database (DB) to fill this gap. This DB holds interactions between individual TFs and their specific targets at a given developmental time. By storing such interactions as a function of developmental progression, we hope to advance the elucidation of regulatory networks that guide lymphocyte development. Besides queries for TF-target gene interactions in developmental stages, the DB provides a graphical representation of downloadable target gene regulatory sequences with locations of the transcriptional start sites and TF-binding sites. The LymphTF-DB can be accessed freely on the web at http://www.iupui.edu/~tfinterx/.

[1]  R. Seong,et al.  E2A/HEB and Id3 Proteins Control the Sensitivity to Glucocorticoid-induced Apoptosis in Thymocytes by Regulating the SRG3 Expression* , 2004, Journal of Biological Chemistry.

[2]  L. Herzenberg,et al.  The regulation of CD5 expression in murine T cells , 2001, BMC Molecular Biology.

[3]  G. Cattoretti,et al.  BCL6 Controls the Expression of the B7-1/CD80 Costimulatory Receptor in Germinal Center B Cells , 2003, The Journal of experimental medicine.

[4]  Ryan T. Phan,et al.  The BCL6 proto-oncogene suppresses p53 expression in germinal-centre B cells , 2004, Nature.

[5]  P. Pandolfi,et al.  Transcriptional Repression of Stat6-Dependent Interleukin-4-Induced Genes by BCL-6: Specific Regulation of Iɛ Transcription and Immunoglobulin E Switching , 1999, Molecular and Cellular Biology.

[6]  L. Garrett-Sinha,et al.  Spi-1 and Spi-B control the expression of the Grap2 gene in B cells. , 2005, Gene.

[7]  J. Monroe,et al.  Transcriptional regulation of the Icam-1 gene in antigen receptor- and phorbol ester-stimulated B lymphocytes: role for transcription factor EGR1 , 1996, The Journal of experimental medicine.

[8]  S. Ley,et al.  Functions of NF-kappaB1 and NF-kappaB2 in immune cell biology. , 2004, The Biochemical journal.

[9]  B. Aronow,et al.  A central role for a single c-Myb binding site in a thymic locus control region , 1995, Molecular and cellular biology.

[10]  M. Bevan,et al.  Notch1 signaling promotes the maturation of CD4 and CD8 SP thymocytes. , 2000, Immunity.

[11]  M. Busslinger.  Transcriptional control of early B cell development. , 2004, Annual review of immunology.

[12]  G. Siu.  Controlling CD4 gene expression during T cell lineage commitment. , 2002, Seminars in immunology.

[13]  S. Desiderio,et al.  Specific recognition of the blk promoter by the B-lymphoid transcription factor B-cell-specific activator protein. , 1994, The Journal of biological chemistry.

[14]  M. Busslinger,et al.  the B-cell-specific transcription factor BSAP . The promoter of the CD 19 gene is a target for , 2022 .

[15]  G. Wildey,et al.  Smad3 potentiates transforming growth factor beta (TGFbeta )-induced apoptosis and expression of the BH3-only protein Bim in WEHI 231 B lymphocytes. , 2003, The Journal of biological chemistry.

[16]  Dana Petterson,et al.  Transcriptional Networks , 2009, Encyclopedia of Database Systems.

[17]  Ellen V Rothenberg,et al.  Regulatory coding of lymphoid lineage choice by hematopoietic transcription factors. , 2003, Current opinion in immunology.

[18]  L. Staudt,et al.  Direct Repression of prdm1 by Bcl-6 Inhibits Plasmacytic Differentiation1 , 2004, The Journal of Immunology.

[19]  Ramana V. Davuluri,et al.  HemoPDB: Hematopoiesis Promoter Database, an information resource of transcriptional regulation in blood cell development , 2004, Nucleic Acids Res..

[20]  J. Goldman,et al.  The role of c-Myb or a related factor in regulating the T cell receptor gamma gene enhancer. , 1995, Journal of immunology.

[21]  L. Staudt,et al.  Control of inflammation, cytokine expression, and germinal center formation by BCL-6. , 1997, Science.

[22]  H. Singh.  Specific recognition site probes for isolating genes encoding DNA-binding proteins. , 1993, Methods in enzymology.

[23]  P. Matthias,et al.  Transcriptional control of B cell development and function. , 2004, Gene.

[24]  Marie-Paule Lefranc,et al.  IMGT , the international ImMunoGeneTics information system , 2003 .

[25]  S. Smale,et al.  Down-regulation of TDT transcription in CD4(+)CD8(+) thymocytes by Ikaros proteins in direct competition with an Ets activator. , 2001, Genes & development.

[26]  G. Wildey,et al.  Smad3 Potentiates Transforming Growth Factor β (TGFβ)-induced Apoptosis and Expression of the BH3-only Protein Bim in WEHI 231 B Lymphocytes* , 2003, The Journal of Biological Chemistry.

[27]  F. Alt,et al.  Gene rearrangement and B-cell development. , 1993, Current opinion in immunology.

[28]  S. Ley,et al.  Functions of NF-?B1 and NF-?B2 in immune cell biology , 2004 .

[29]  M. Sigvardsson,et al.  EBF and E47 collaborate to induce expression of the endogenous immunoglobulin surrogate light chain genes. , 1997, Immunity.

[30]  J. Leiden,et al.  Transcriptional regulation of T lymphocyte development and function. , 1999, Annual review of immunology.

[31]  Ellen V Rothenberg,et al.  Definition of regulatory network elements for T cell development by perturbation analysis with PU.1 and GATA-3. , 2002, Developmental biology.

[32]  K. Georgopoulos.  Haematopoietic cell-fate decisions, chromatin regulation and ikaros , 2002, Nature Reviews Immunology.

[33]  Juan Mata,et al.  Correlations between gene expression and gene conservation in fission yeast. , 2003, Genome research.

[34]  Lineage-specific regulation of the murine RAG-2 promoter: GATA-3 in T cells and Pax-5 in B cells. , 2000 .

[35]  M. Busslinger,et al.  The transcription factor BSAP (NF-HB) is essential for immunoglobulin germ-line epsilon transcription. , 1994, Journal of immunology.

[36]  Obi L. Griffith,et al.  ORegAnno: an open access database and curation system for literature-derived promoters, transcription factor binding sites and regulatory variation , 2006, Bioinform..

[37]  G. Gibson,et al.  Microarray Analysis , 2020, Definitions.

[38]  K. Johnson,et al.  An interleukin-2 signal relieves BSAP (Pax5)-mediated repression of the immunoglobulin J chain gene. , 1996, Immunity.

[39]  Harinder Singh,et al.  Contingent gene regulatory networks and B cell fate specification. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[40]  R. Hardy.  B-cell commitment: deciding on the players. , 2003, Current opinion in immunology.

[41]  M. Fallahi-Sichani,et al.  Analysis of Transcription Factor Expression during Discrete Stages of Postnatal Thymocyte Differentiation1 , 2004, The Journal of Immunology.

[42]  A. Rolink,et al.  Transcriptional networks in developing and mature B cells , 2005, Nature Reviews Immunology.

[43]  J. Sgouros,et al.  Microarray analysis of orthologous genes: conservation of the translational machinery across species at the sequence and expression level , 2002, Genome Biology.

[44]  M. Kubo,et al.  A Putative Silencer Element in the IL-5 Gene Recognized by Bcl61 , 2002, The Journal of Immunology.

[45]  L. Staudt,et al.  BCL-6 represses genes that function in lymphocyte differentiation, inflammation, and cell cycle control. , 2000, Immunity.

[46]  Tatiana A. Tatusova,et al.  Entrez Gene: gene-centered information at NCBI , 2004, Nucleic Acids Res..

[47]  Lisa M. Toney,et al.  Inhibition of Th2 Differentiation and GATA-3 Expression by BCL-6 1 , 2003, The Journal of Immunology.

[48]  M. Bevan,et al.  Correlating notch signaling with thymocyte maturation. , 1998, Immunity.

[49]  A. Mui,et al.  STAT5 as a molecular regulator of proliferation, differentiation and apoptosis in hematopoietic cells , 1999, The EMBO journal.