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I am new to bioinformatics, my background is in Electrical Engineering. I am trying to convert Affymetrix Cotton Probe IDs to gene symbols. I have a gene expression dataset and I need the expressions for only certain genes. So in the dataset, I have a probe id such as Ghi.10301.1.S1_s_at, how can I get the gene symbol associated with it? Thanks

EDIT: This is the specific dataset I am looking at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE50770

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  • $\begingroup$ So which file are you trying to parse? Is it GSE50770_series_matrix.txt? The link you gave has various resources associated with it . $\endgroup$ – terdon Jul 13 '18 at 8:32
  • $\begingroup$ One problem you may face is with the state of the cotton genome (Gossypium hirsutum) itself, there are no gene symbols for this genome, you're stuck with accession IDs for each probe, which the provided Affymetrix annotation file has some information on via homology to other characterised proteins and coding sequences, that's about it! The official genome annotation is not much use either! $\endgroup$ – Matt Bashton Jul 24 '18 at 13:25
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Your dataset was produced on a microarray. The probe IDs in the FASTA file are similar to read IDs produced from other NGS experiments like RNA-Seq. According to the workflow provided by Ensembl the first step is to align your reads to a reference. You'll only keep the reads that match the reference completely. Once the probes are aligned you'll be able to quantify the number of reads mapping to the gene that the probe was designed to attract.

I did find a file providing the database entries associated with each probe ID (one of which is the ID you provided) for the Affymetrix Cotton Genome Array.

probe microarray workflow

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    $\begingroup$ Hi @kohlkopf thanks for your response. I don't need to quantify the reads here, since I already have expression values for different genes in the dataset. What I am trying to do is convert the Probe IDs to gene symbol so I can extract the data for a specific subset of genes I am interested in. I will add a link of the data set I am looking at on the original post. $\endgroup$ – Adi Jul 12 '18 at 22:37
  • $\begingroup$ This is demonstrably not the answer to the OPs question, the OP has not got a FASTA file of probe sequences, equally the hits < 100 step and "quantify the number of reads mapping to the gene" - would only be appropriate for a RNASeq experiment, in this case expression is via probe intensity measurements not read count, counting the number of probes would simply be a bad proxy for gene length. This is simply an ID mapping issue. $\endgroup$ – Matt Bashton Jul 24 '18 at 13:05
  • $\begingroup$ Mapping to Ensembl won't help either as it only has the Gossypium raimondii genome were as the Affy Cotton array is based on Gossypium hirsutum. $\endgroup$ – Matt Bashton Jul 24 '18 at 13:10
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The first stop for decoding probe IDs for a microarray platform is usually the GEO Platform Description: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GPL8672

This description contains a table of annotation, and is provided (in this instance) by the array manufacturer. You can view, or download, the full table: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?view=data&acc=GPL8672&id=1538&db=GeoDb_blob35

GEO Platform annotations do date, and so for up-to-date annotations, download from NetAffx: http://www.affymetrix.com/support/technical/byproduct.affx?product=cotton

The most recent annotations (dated 2016-04-13) are available here: http://www.affymetrix.com/Auth/analysis/downloads/na36/ivt/Cotton.na36.annot.csv.zip.

For the example in your question, looking at this probe in the CSV:

"Ghi.10301.1.S1_s_at","Cotton Genome Array","Gossypium hirsutum","Mar 30, 2016","Consensus sequence","GenBank","Ghi.10301.1","gb:DT050231 /DB_XREF=gi:72275634 /DB_XREF=COT_DW_H07 /TID=Ghi.10301.1 /CNT=21 /FEA=EST /TIER=ConsEnd /STK=1 /UG=Ghi.10301 /UG_TITLE=Transcribed locus, moderately similar to NP_568148.1 ubiquitin conjugating enzyme ubiquitin-like activating enzyme (Arabidopsis thaliana) /REP_ORG=G. hirsutum","DT050231","Ghi.10301","Ghi.10301","---","---","---","---","---","est","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","---","This probe set was annotated using the Accession mapped clusters based pipeline to a UniGene identifier using 21 transcripts. // false // Accession mapped clusters // E","AI730871,DN803875,DR452973,DR457278,DT050231,DT545642,DT546719,DT546982,DT546983,DT547780,DT547781,DT555433,DT559909,DT564450,DT566924,DT569293,DT569974,DT571307,DT571318,DT571472,DT573548","AI730871 // /DB_XREF=BNLGHi8130 // gb // --- // --- /// DN803875 // /DB_XREF=G.hir-8-10 DAA bolls drought stressed751 // gb // --- // --- /// DR452973 // /DB_XREF=CM008C10 // gb // --- // --- /// DR457278 // /DB_XREF=CM053F01 // gb // --- // --- /// DT050231 // /DB_XREF=COT_DW_H07 // gb // --- // --- /// DT545642 // /DB_XREF=EST1056282 // gb // --- // --- /// DT546719 // /DB_XREF=EST1057359 // gb // --- // --- /// DT546982 // /DB_XREF=EST1057622 // gb // --- // --- /// DT546983 // /DB_XREF=EST1057623 // gb // --- // --- /// DT547780 // /DB_XREF=EST1058420 // gb // --- // --- /// DT547781 // /DB_XREF=EST1058421 // gb // --- // --- /// DT555433 // /DB_XREF=EST1066073 // gb // --- // --- /// DT559909 // /DB_XREF=EST1070549 // gb // --- // --- /// DT564450 // /DB_XREF=EST1075090 // gb // --- // --- /// DT566924 // /DB_XREF=EST1077564 // gb // --- // --- /// DT569293 // /DB_XREF=EST1079933 // gb // --- // --- /// DT569974 // /DB_XREF=EST1080614 // gb // --- // --- /// DT571307 // /DB_XREF=EST1081947 // gb // --- // --- /// DT571318 // /DB_XREF=EST1081958 // gb // --- // --- /// DT571472 // /DB_XREF=EST1082112 // gb // --- // --- /// DT573548 // /DB_XREF=EST1084188 // gb // --- // ---","---"
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