Supplementary material for TissueInfo
TissueInfo: high-throughput identification of tissue expression profiles and specificity.
This page offers the data sets we used to evaluate TissueInfo. This information is freely available so that others can use it to verify the evaluation of our method, or benchmark new methods under the same conditions.
Additional information, such as licensing information, documentation (for both end-users and developers who wish to reuse TissueInfo) is available from our Institute's Computational Research Tool Directory.
The evaluation data set is given in the table below. The data is offered in
two formats. HTML format is suitable for browsing the information. XML files
are suitable for parsing the information with computational tools. Each row
of the table contains groups of gene extracted from SWISS-PROT such that
they are likely to be specific to the tissue shown in the first column.
The exact procedure used to extract these genes from SWISS-PROT is described
in more detail in the paper.
During the evaluation, we found 25 SWISS-PROT entries which did not agree
with the primary literature that they reference (i.e. tissue specificity
annotations were misleading, inaccurate, or inconsistent when compared to
the articles referenced by the entry.) The accession numbers of these
entries are:
2A5B
ATF2
BACE
BASP
BIEA
BIR6
CHLR
CRF1
DLG4
EAT1
FETB
FMO1
FMO5
GP37
GSHG
GSUB
HMCM
I5P1
NPT2
P2Y4
PGCV
QOR
RSMN
SN25
V2R
Each accession number is linked to a text view of the SWISS-PROT entry obtained at
the time we did the evaluation. This table
identifies the inconsistencies or inaccuracies found in each of these
entries.
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