Probing the Xenopus laevis inner ear transcriptome for biological function

BMC Genomics

Table 5 Summary of gene compilation and analysis methods

Gene group	Xl-PSIDs	HGNC symbols	Method of compilation	Sequence similarity mapping	DAVID analysis
IET	453	594*	Scientific literature [22–27, 42, 85]	All	Yes
DF	139	157*	Keyword query (OMIM database)	All	No
IC	74	210*	Scientific literature [66, 88–90]	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

The number of Xl-PSIDs in all inner ear gene categories (IET, DF, IC, IT, pTF) and in the 10^th 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.

ISSN: 1471-2164