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I have a list of genes for each of which I'd like to find:

  1. A list of transcription factors that up-regulate the gene

  2. A list of inhibitory factors that down-regulate it.

I used this tool on Qiagen's website to find transcription factors (and will be thrilled if someone can share a better tool). Its less than ideal for my purposes because I need to search each gene individually and there doesn't seem to be anyway of downloading or copy/pasting the transcription factors it returns; but it works.

What I really need now though, is a way to find inhibitory factors by gene. Does anyone know how I can do this?

I have already tried using wikipathways and found it to show almost none of the transcription factors I found on Qiagen's website leading me to conclude that their data is far from comprehensive. I have applied for access to Ingenuity only to discover that I will not be granted access soon enough to make use of it.

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    $\begingroup$ I don't think such a tool exists simply because there are too many interactions possible. They also depend on the cell type, state of the cell and so on. I have been working with a transcription factor for quite a while and I would have loved such a tool. We endet up analyzing new targets ourself. $\endgroup$ – Chris Dec 11 '14 at 22:09
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    $\begingroup$ There is no tool and there is no direct way. There are databases that have predicted transcription factor binding sites (TFBS). There are experimental data (ChIP-seq) for TFBS too; however it is difficult to ascertain if the TF is activator or repressor without further experimentation. Moreover, same TF can act as either repressor or activator in different circumstances. $\endgroup$ – WYSIWYG Dec 12 '14 at 6:28

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