Question: extracting chip id for a transcription factor
0
gravatar for F
3.6 years ago by
F3.3k
Iran
F3.3k wrote:

hello guys,

how i can extract chip id for a transcription factor for example one of BES1 family please?

sequence gene • 1.1k views
ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by F3.3k
1

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

ADD REPLYlink written 3.6 years ago by Sean Davis25k

 

"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...

ADD REPLYlink written 3.6 years ago by F3.3k
3
gravatar for Alexander Skates
3.6 years ago by
United Kingdom
Alexander Skates320 wrote:

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.

ADD COMMENTlink written 3.6 years ago by Alexander Skates320

thank you very much for your detailed explanation, you all right about the paper and my purpuse

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by F3.3k

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?

ADD REPLYlink written 3.6 years ago by F3.3k
1

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)

ADD REPLYlink modified 3.6 years ago • written 3.6 years ago by Alexander Skates320
1
gravatar for F
3.6 years ago by
F3.3k
Iran
F3.3k wrote:

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

ADD COMMENTlink modified 3.6 years ago • written 3.6 years ago by F3.3k
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