Problem facing for retrieving Phalanx_id from geo data set in R
Hi
I am facing a lot of problem for retrieving Phalanx_id to gene symbol .My geo data i downloaded from geo dataset and stored in a excel file.Where the first column of my data set is ID_REF as bellow and rest of the column are the sample id lke GSM2527022
PH_hs_0000002
PH_hs_0000003
PH_hs_0000004
PH_hs_0000005
PH_hs_0000006
PH_hs_0000007
PH_hs_0000008
PH_hs_0000009
PH_hs_0000010
PH_hs_0000011
PH_hs_0000012
PH_hs_0000013
PH_hs_0000014
PH_hs_0000015
PH_hs_0000016
PH_hs_0000017
PH_hs_0000018
There is almost 31741 ID_REF. so how can i convert them into gene symbol?
1 answer
Did you look at the files that were linked? The NCBI GPL file link (was in last post, posted again) contains a mapping of ID's you have and Gene Names. You can download the table, read it into R and then select the two columns you need (ID and Gene_Symbol, excerpt below)
ID Group Entrez_gene REFSEQ GB_ACC RNA_nucleotide_gi Protein_accession.version Gene_symbol Description Chromosome Map_location Genomic_Specific Orientation GO_id_function GO_id_componen GO_id_process GO_term_function GO_term_component GO_term_process Ensembl_gene Ensembl_transcript Ensembl_protein Unigene_cluster Uniprot_id SEQUENCE SPOT_ID
PH_hs_0000002 1 1089 NM_001817.2 NM_001817.2 71143131 NP_001808.2 CEACAM4 carcinoembryonic antigen-related cell adhesion molecule 4 19 19q13.2 No - GO:0005624,GO:0005887,GO:0016020 membrane fraction,integral to plasma membrane,membrane ENSG00000105352 ENST00000456892,ENST00000472081,ENST00000221954 ENSP00000403837,ENSP00000221954 Hs.12 O75871 AACTATTCAAGCCTATTATTGGCACAAGGGGAAAACGGCAGAAGGGAGCCCTCTCATTGC
PH_hs_0000003 1 4049 NM_001159740.1 NM_001159740.1 229092380 NP_001153212.1 LTA lymphotoxin alpha (TNF superfamily, member 1) 6 6p21.3 No + GO:0005102,GO:0005125,GO:0005164,GO:0005515 GO:0005576,GO:0005615,GO:0016020 GO:0006917,GO:0006959,GO:0007165,GO:0007267,GO:0007584,GO:0032496,GO:0048147,GO:0048535 receptor binding,cytokine activity,tumor necrosis factor receptor binding,protein binding extracellular region,extracellular space,membrane induction of apoptosis,humoral immune response,signal transduction,cell-cell signaling,response to nutrient,response to lipopolysaccharide,negative regulation of fibroblast proliferation,lymph node development ENSG00000226275,ENSG00000226979,ENSG00000238130,ENSG00000223919,ENSG00000173503,ENSG00000231408,ENSG00000230279 ENST00000473355,ENST00000412851,ENST00000464086,ENST00000426845,ENST00000464821,ENST00000441939,ENST00000487391,ENST00000432632,ENST00000490708,ENST00000383304,ENST00000476761,ENST00000383303,ENST00000461499,ENST00000454550,ENST00000479906,ENST00000436519,ENST00000468015,ENST00000448630,ENST00000466460,ENST00000456789,ENST00000471842,ENST00000418386,ENST00000489638,ENST00000454783,ENST00000498217,ENST00000383499,ENST00000481446,ENST00000400272 ENSP00000412555,ENSP00000402413,ENSP00000387924,ENSP00000416337,ENSP00000372793,ENSP00000372791,ENSP00000416509,ENSP00000395976,ENSP00000407133,ENSP00000395895,ENSP00000413450,ENSP00000403495,ENSP00000372991,ENSP00000383131 Hs.36 P01374,Q5STV3 GTGAGAGGGCATGCGCACAAGGCTGACCAAGAGAGAAAGAAGTAGGCATGAGGGATCACA
PH_hs_0000004 1 38 NM_000019.3 NM_000019.3 223890189 NP_000010.1 ACAT1 acetyl-CoA acetyltransferase 1 11 11q22.3-q23.1 Yes + GO:0003985,GO:0005515,GO:0008415,GO:0016740,GO:0046872 GO:0005739,GO:0005743,GO:0005759 GO:0008152 acetyl-CoA C-acetyltransferase activity,protein binding,acyltransferase activity,transferase activity,metal ion binding mitochondrion,mitochondrial inner membrane,mitochondrial matrix metabolic process ENSG00000075239 ENST00000265838 ENSP00000265838 Hs.232375 P24752 CATGCTAATTCAGAAGCTGTAGACAACCTCTGCTATTTAAGGAGACAACCCTATGTGACC
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Problem for retrieving gene symbol from ID_REF
I gave the post again because i am still now unable to retrieve my gene symbol from that ID_REF by R