It seems to be a basic question, but I couldn't find a certain answer.

The human genome is known for more than a decade, and is available through several data providers as the NCBI etc. For the genes' promoters however there seems to be much less information. There are some characteristics known (like the TATA box, which appears in ~25% of human genes), some prediction methods (like CpG sites appearance), some rough estimations for the location (100-1000kbp long, in the adjacent 2kbp upstream from the TSS), but I couldn't find any data set with a closed list of human genes' promoters.

Is this really yet to exist?

  • 1
    $\begingroup$ Not 100%. People are still working on it using by studying nucleosome positioning and transcription factor binding sites and other factors. For many ncRNAs, even the TSS is not well annotated. Techniques like CAGE are quite recent. But you should clarify what you really mean by promoter: the minimal promoter (TATA-box etc) or all TFBS? $\endgroup$
    Oct 8 '16 at 9:24
  • $\begingroup$ @WYSIWYG Thanks! I'm looking for the whole TFBS (as far as I understand). What I'm doing is comparing and trying to optimize CpG islands (CGIs) identifying algorithms (e.g. as Takai's, and recent CpG clustering algorithm). One major parameter for scoring is how well do results lay withing promoters. Sort of chicken and egg situation. Do you happen to know if CpG methylation suppresses expression only when appears within the promoter area, or in it's surroundings as well (up/downstream) $\endgroup$
    – galra
    Oct 8 '16 at 11:19

Nope. The human genome is still quite unexplored, new genes are still being discovered and the annotation of non-protein-coding regions (that include promoters) is still far from being complete. For example, look at the Statistics comparison of the current and previous Human GENCODE Release, it clearly shows that the annotation of the human genome is still an ongoing process.


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