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Transcription Factor Graph in Prolog (view source)
Revision as of 13:16, 27 October 2021
, 13:16, 27 October 2021added schematic diagram of finding promoter from TSS
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==Transcription Start Sites (TSS)==
==Transcription Start Sites (TSS)==
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+[[File:TSS promoter schematic.png|thumb|right|500px|Schematic example of locating gene promoter region from -1000bp to +1000bp of TSS for 2 genes, one on "+"-strand and one on "-" strand.]]
Chromosomal positions were tabulated for regions of human chromosomes corresponding to 1000 bp upstream and 1000 bp downstream of TSS for 21857 genes. The choice of TSSs is inspired by Jonathan Dennis's nucleosome mapping projects.
Chromosomal positions were tabulated for regions of human chromosomes corresponding to 1000 bp upstream and 1000 bp downstream of TSS for 21857 genes. The choice of TSSs is inspired by Jonathan Dennis's nucleosome mapping projects.
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* if on (+)-strand, TSS is ChromStart, upstream ChromStart-1000 to downstream ChromStart+1000.
* if on (+)-strand, TSS is ChromStart, upstream ChromStart-1000 to downstream ChromStart+1000.
* if on (-)-strand, TSS is ChromEnd, downstream ChromEnd-1000 to upstream ChromEnd+1000 (note orientation is flipped)
* if on (-)-strand, TSS is ChromEnd, downstream ChromEnd-1000 to upstream ChromEnd+1000 (note orientation is flipped)
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3. Save copy as scg3_copy.bed.plusminus1000.xlsx with additional columns for TSS, 1000 bp upstream and 1000 bp downstream (with postions all on the (+)-strand)
3. Save copy as scg3_copy.bed.plusminus1000.xlsx with additional columns for TSS, 1000 bp upstream and 1000 bp downstream (with postions all on the (+)-strand)