ChIP-chip

Contents The ChIP-chip table is designed to provide information on in vivo binding DNA fragments. The collected DNA fragments are based on the results of "ChIP-on-chip" experiments that combine in vivo Chromatin Immuno-Precipitation (ChIP) with various microarray technologies (chip). Examples of the currently included data: Sp1, c-Myc and p53 in vivo binding sites were defined in the following way: chromatin-immunoprecipitated DNA was hybridized with human Chromosome 21 and 22 high-density tiled arrays, probes of 25 bp separated by 35 bp in average (Kapranov et al, Science, 2002, v.296, p.916-919). CREB1 and NF-kappaB p65 (RelA) in vivo binding sites were defined in a different array: chromatin-immunoprecipitated DNA was hybridized with human Chromosome 22 microarray slides, probes ranging in size from 300 bp to 1400 bp (Rinn et al, Genes Dev, 2003, v.17, p.529-540). The ChIP-chip table is interlinked with other TRANSFAC® tables (Gene, Factor, Cell, Reference) where more details about the corresponding entities can be found. In addition to binding fragments we provide information about closely located genes. Please note, genes have been associated with the fragments just according to their close location to the in vivo binding DNA fragments. To provide information about the closely located genes we mapped DNA fragments on the sequence build HSA_May2004 and then looked for annotated TSS and exons within a window of 150 kb on both sides of the fragment. On both sides the feature (TSS or exon) with the smallest distance to the fragment was chosen, and the respective gene was assigned to the fragment as "nearest gene". This procedure resulted in one, two, or no genes associated with each fragment. Other in vivo binding DNA-fragments identified by distinct microarray technologies, like, for example, CpG island array, different promoter arrays, are planned to be included in the next releases of TRANSFAC®.

Fields

It should be noted that in individual entries some fields may be empty. In this case, these fields are not displayed.

ChIP-chip summary   General information about the ChIP-chip entry: number of linked transcription factors, external database links and of references. AC Accession number   "FR" + 7-digit number AS Accession numbers, secondary   when two or more entries are merged, the additional accession numbers, separated by commas, are stored in this field ID Identifier   "FR" + 7-digit number DT Created Updated   Date of entry creation; entry author Date of last entry updating; updater DE Description   GENE accession no. Genes located within 150 kb on both sides of the fragment. One "nearest gene" on each side of the fragment is shown. OS Species   Biological species OC Taxonomic classification   Systematic biological classification of the species SQ Sequence   Sequence of the ChIP-chip DNA fragment Capital letters indicate probes (PUBMED: 15082775, PUBMED: 14527995) or binding fragments as authors defined them (PUBMED: 14980218) and small letters indicate flanks added by TRANSFAC team SC Sequence Source   Sequence build; Chromosome number; Position1-position2 (absolute positions on the chromosome); FORWARD/REVERSE (strand information) BF Binding factors   Factors shown to bind the DNA fragment in vivo (linked accession number; name; "Quality" of the factor-fragment interaction; biological species of the factor; Cellular source (where in vivo binding was shown): linked accession number; short description). MM Method(s)   Methods applied for the identification of the fragment DR External database links   EMBL: accession number; identifier (first site position:last site position) RN Reference number   [Consecutive entry reference number]; Reference accession number. RX PUBMED; link to PubMed entry. RA Reference authors Authors (NOTE: accents are omitted, German umlauts are transcribed as follows: ä -> ae, ö -> oe, ü -> ue; German "s-z" (ß) -> ss) RT Reference title Reference Title (NOTE: Greek letters are expanded to alpha, beta, gamma etc.) RL Reference source Journal Volume:Pages (year)