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Tip: This table lists computational prediction of CREB binding sites (CREs). To quickly search the same gene in another data set (e.g. ChIP-chip, cAMP induced genes in tissues), click the links from the last column. The locuslink number will be used as query.
|No||Symbol||Gene Name||Accession||LocusLink||Alias Symbols||CRE Prediction||CRE Flag||Full Site||Half Site||Conserved CRE||CREcluster||pHMM+Pos||Chrom||Strand||Pos||Note||Link|
|1||HOXD9||homeo box D9||NM_014213||3235||HOX4;HOX4C;Hox-4.3;Hox-5.2||others||none||chr2||+||177189631||"all, "||HEK293T_Expression Human_ChIP_chip Pancreatic_Islet_Expression|
Computational prediction of functional CREs on promoters of human RefSeq genes.
The names for most columns are self-explanatory; Details about columns for computational results are listed below:
CRE Prediction: Genes with predicted functional CRE by any of the three methods (conserved CRE, CRE cluster, or positional conserved pHMM hits) are chosen and further separated into two groups, CRE_TATA and CRE_NoTATA based on the presence of TATA boxes. The rest of the genes are simply labeled as "others". When a gene (defined as unique LocusLink number) has multiple entries (GenBank Accession numbers) due to different splicing forms, the best prediction for CRE is chosen
CRE Flag: Flags, or markers for the types of CREs on the promoter (-3Kb to 300bp from transcription start site). "F/f" means full site, "H/h" means half site, with upper case representing conserved CRE. "FH" is a full site CRE in the species studied but only appear as half site in other species. "T/t" at the end means the presence of a TATA box less than 300bp downstream of the CRE.
Full Site/Half Site: All occurrences of full site (TGACGTCA) or half site(TGACG/CGTCA) CREs in -5Kb-1Kb region of the transcription start site (TSS). Here the position of each CRE relative to the TSS is shown following its flag.
Conserved CRE: All the conserved full and half site are shown in this column since they are the most likely functional CREs. These CREs are shown similar to the format used by Full site/Half site, with the addition of the distance to closest downstream TATA box, shown as the last number.
CRECluster: Here all the CRE clusters are shown; In a CRE cluster, neighbors must be closer than 50bp to each other; If more than two clusters appear in a promoter, they are separated by "|".
pHMM+Pos: If there is a positional conserved CRE identified by pHMM search in human and mouse orthologs, it will be shown here. The values shown are 1) models used(F: full site model; H: half site model) in human and mouse, respectively; 2) Human match score and position; 3) Mouse match and position. Here the position is relative to the start codon.
Chrom/Strand/Pos: Chromosomal position of the TSS and the strand of
the transcript based on hg16 human genome assembly from the UCSC
Genome Bioinformatics Site.