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Due to the fact that the measurement identifiers are mapped to different string values instead of simple small numbers, the URL size fluctuates and increases rapidly depending on the requested measurements.
These identifiers are mapped to the gene designations used in SubtiWiki and the Uniprot identifiers in an Excel table.
Affymetrix probe identifiers are mapped to UCSC Genome Browser known genes and these data were retrieved from the table named knownToGnfAtlas2.
Since there are currently no HMM models for Pfam-B domains, BLAST [ 13] searches are performed against the ProDom protein sequence database [ 14, 15], and the detected ProDom identifiers are mapped to corresponding Pfam-B accessions.
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The profiles from either experiment identified by probe set identifiers were mapped to the Ensembl 39 gene_stable_ids.
Among the 86 identifiers that represent the 56 DEP's that were identified from human pituitary adenoma tissues, 75 identifiers were mapped to the corresponding molecules (genes; proteins) except for 11 identifiers (Additional file 1, Table S2).
Among the 154 identifiers that represented the 111 proteins that were identified from human pituitary adenoma tissue, 147 identifiers were mapped to the corresponding molecules (genes; proteins), except for 7 identifiers (Additional file 1, Table S1).
Original Illumina probe identifiers were mapped to Entrez gene IDs using the Bioconductor illuminaHumanv3.db annotation package for Illumina HT-12 v3 arrays obtaining log2 intensity values for a total of 19,761 genes.
Unigene identifiers were mapped to Entrez identifiers, resulting in 502 probes of the custom, Entrezgene-based CDF file (Additional file 2: Supplementary table).
All gene identifiers were mapped to ENSEMBL gene IDs.
UniProt identifiers were mapped to HGNC identifiers using the cross references in the full UniProt entries.
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