extracting chip id for a transcription factor

Question

[zizigolu]

Hello guys,

How can I extract chip id for a transcription factor for example one of BES1 family please?

[Sean Davis]

What do you mean by "chip id"? What is "example one"?

[zizigolu]

Eight cotton BES1 genes (BRTF's) were selected from the Plant TFDB (http:// planttfdb.cbi.pku.edu.cn) for network analysis and their chip Ids were extracted from Plexdb tool (http://www.plexdb.org/).

This is the exact sentences from a paper that I didn't get to do my procedure based on...

Answer 1

[Alexander Skates]

You're inferring a transcriptional network using ARACNe, correct? Then the chip ID you need entirely depends on what chip your microarray data comes from. Given that you appear to be using this paper for reference, you need to convert it to the probe ID for the Affymetrix Cotton Genome Array.

Searching the Plant TFDB for BES1 yields this result. Scroll down to the "Expression" information, and it gives you the GeneVestigator ID 259955_s_at, which happens to be the probeset ID for the Affymetrix Arabidopsis ATH1 Genome Array.

Now go to the PLEXdb Blast, input the Arabidopsis ID, specify the Arabidopsis ATH1 22k, and then indicate that you want to covert it to the Cotton platform. The top result is Ghi.9165.1.S1_s_at, and checking this against the annotation provided by Affymetrix themselves this seems to be correct.

[zizigolu]

Thank you very much for your detailed explanation, you're right about the paper and my purpose

[zizigolu]

I did your proposed steps but may I ask please from this part of article

Firstly we have taken BRTF's from cotton transcription factor database (http://www.bmicc.org/web/english/search/planttfdb) then we perform blastn with the sequences of cotton affymetrix chip where we found total 8 BES1 genes

Could not I retrieve the BSE1 TF without doing previous steps?

[Alexander Skates]

Sorry, I'm not entirely sure what you're asking here - whether you can get the IDs of the TF through performing blastn on the sequence of the gene rather than converting the probe ID?

(If this is what you're asking, PlantTFDB links to the NCBI GenBank entry under the heading "Annotation -- Nucleotide", from which you can get the FASTA sequence to blast in PLEXdb)

[zizigolu]

Yes I asked the exact you guessed...then I can get the TF in two ways: performing blastn and converting the probe ID

Then in paper the author mentioned two ways to get TF by both I can get TF id

Thank you