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Table 5 Summary of gene compilation and analysis methods

From: Probing the Xenopus laevis inner ear transcriptome for biological function

Gene group Xl-PSIDs HGNC symbols Method of compilation Sequence similarity mapping DAVID analysis
IET 453 594* Scientific literature [2227, 42, 85] All Yes
DF 139 157* Keyword query (OMIM database) All No
IC 74 210* Scientific literature [66, 8890] All No
IT 180 130 Keyword query (Affymetrix annotation file) and scientific literature Subset (IC) No
pTF 795 790* Keyword query (NetAffx™ analysis center and Xenbase) ---- Yes
10 th equal tally decile 1218 ---- Rank ordered top 10% based on number of Xl-PSIDs ---- Yes
10 th equal intensity decile 40 ---- Rank ordered based on intensity value range ---- Yes
  1. The number of Xl-PSIDs in all inner ear gene categories (IET, DF, IC, IT, pTF) and in the 10th deciles are reported together with compilation and analysis methods for each gene group. The table reports the number of symbols for HGNC proteins that formed affirmative pairwise alignments with Xl-PSID consensus sequences through sequence similarity mapping (TBLASTN). *HGNC symbols were linked to more than one Xl-PSID, resulting in a number that is higher than the number Xl-PSIDs.