I am trying to find out which transcription factors or enhancers might be involved in regulation of expression of a set of genes in lung cancer. Let me know if there is any good resource for that.
I would use http://amp.pharm.mssm.edu/Enrichr/ for this, in which you use your list of genes as input and go look for overrepresented transcription factors and motifs.
One of the best updated database I have seen is http://yeastmine.yeastgenome.org/yeastmine/bag.do . Upload your list there and you can do exactly what you have asked.
For curated regulators and their targets the easiest and quickest way to access yeast data is with powerful search tool, YeastMine (http://yeastmine.yeastgenome.org/yeastmine/begin.do). Using the ‘Lists’ option on the top menu, you can upload your list of transcription factors, using the ‘Upload’ option on the far left-hand side, next to ‘View’. Just type or paste your identifiers into the search box, or upload the list using the ‘Choose File’ button, below the box. After you click the ‘Create List’ button, you can rename the list in the ‘Choose a name for the list’ box at the top of the page. You can also save this list for future use by creating a ‘MyMine’ account (click ‘Log in’ and create an account using OpenID or a google account).
After creating the list, click on the ‘Templates’ option (to the left of ‘List), and use the filter box to search for ‘target’. You should see 3 templates — select the ‘Gene(regulator)->Gene(targets)’ template. Then select the checkbox next to ‘constrain to be IN saved Gene list’ and select the list you just created from the pulldown. Click ‘Show results,’ which will bring you to a results table that will show you all the gene targets that we have curated for your list of genes.
If you haven’t used YeastMine, we have some nice help videos on how get started here: https://www.youtube.com/playlist?list=PL0VHJdmmIuj-b00aNRfqwMe9TvkfWWcyZ. For what I described, video #3 and video #9 on the YeastMine playlist would be most useful.
Another resource is Yeastract (http://www.yeastract.com/). There is a form where you can copy and paste a list of transcription factors and it should return the targets (http://www.yeastract.com/formfindregulated.php).
I think this post gives a good overview: Best Database Of Transcription Factor Binding Sites
ENCODE ChIP-Seq Significance Tool is the tool for this purpose. http://encodeqt.simple-encode.org/
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Similar question here: Finding the TFs that regulate a set of genes
If you could upload your list as a network in cytoscape, there is iRegulon app there that would find which TFs enriched in upstream motifs of your genes
ChIPBase is developed to explore the transcriptional regulatory relationships between TFs and Genes from ChIP-seq data (currently contain over 10,200 samples). It also provides the co-expression patterns between TFs and Genes form ~1,8000 RNA-seq expression data (from TCGA data and GTEx data). Now it has been updated to version 2 and published on NAR titled ChIPBase v2.0: Decoding Transcriptional Regulatory Networks of Non-coding RNAs and Protein-coding Genes from ChIP-seq Data. Here is the website (http://rna.sysu.edu.cn/chipbase). I hope this will help you.