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Table 1 The first five genomic segments significantly over−/underexpressed in the Thyroid (Pool A) transcriptome map and in the Thyroid (Pool A) vs. Pool of non-thyroid tissues (Pool B) transcriptome map

From: A molecular view of the normal human thyroid structure and function reconstructed from its reference transcriptome map

Thyroid transcriptome map

Chra and Location

Segment Startb

Segment Endb

Value A

q-value

Genes in the segmentc

Overexpressed segments

 chr8

 8q24.22

134,000,001

134,500,000

1,040.20

0.0033

TG, Hs.654670, NDRG1

 chr16

 16q12.2

56,500,001

57,000,000

907.10

< 0.0001

MT2A, MT1E, MT1A, MT1F, MT1G, MT1H, MT1X, HERPUD1

 chr1

 1p21

103,750,001

104,250,000

768.87

0.0009

AMY2B, AMY2A, AMY1B

 chr11

 11q13.1

65,000,001

65,500,000

763.28

0.0001

NEAT1, Hs.736281, Hs.593027, MALAT1, Hs.712678, Hs.732685

 chr4

 4q13

70,500,001

71,000,000

689.99

0.0021

STATH, HTN3, HTN1

Thyroid vs. Pool of non-thyroid tissues transcriptome map

Chra and Location

Segment Startb

Segment Endb

Value A/B

q-value

Genes in the segmentc

Overexpressed segments

 chr8

 8q24

134,000,001

134,500,000

30.57

0.0024

TG, Hs.654670, ST3GAL1

 chr14

 14q13.2-q13.3d

36,500,001

37,000,000

13.47

< 0.0001

MBIP, SFTA3, Hs.715763, NKX2-1

 chr6

 6q25.1d

150,250,001

150,750,000

11.15

0.0005

Hs.15422, PPP1R14C, IYD

 chr2

 2q12-q14.1

113,750,001

114,250,000

6.76

0.0045

PAX8, Hs.656634, Hs.675465

 chr8

 8q23

110,500,001

111,000,000

5.17

< 0.0001

PKHD1L1, Hs.88651, EBAG9, Hs.632960

Underexpressed segments

 chr2

 2p12

79,000,001

79,500,000

0.17

0.0001

REG1B, REG1A, REG3A

 chr18

 18q12.1

28,500,001

29,000,000

0.27

0.0002

DSC3, Hs.557559, DSC1, DSG1

 chr1

 1q21-q22

153,000,001

153,500,000

0.29

< 0.0001

SPRR1B, SPRR2D, SPRR2A, LELP1, LOR, S100A, S100A7

 chr5

 5q32

147,250,001

147,750,000

0.30

< 0.0001

SCGB3A2, C5orf46, SPINK5, SPINK7

 chr10

 10q26.11

118,000,001

118,500,000

0.33

0.00087

PNLIP, PNLIPRP1, PNLIPRP2

  1. Analysis was performed using default parameters (see Methods section). Overexpressed segments are sorted by decreasing expression values in the thyroid transcriptome map; underexpressed segments are sorted by increasing expression values. In the ‘Map’ mode, TRAM displays UniGene EST clusters (with the prefix “Hs.” in the case of H. sapiens) only if they have an expression value. For simplicity, some segments are not shown because they overlap with those highlighted in one of the listed regions. In bold the genes with a statistically significant over- or underexpression values in the segment. The complete results for these models are available as online supplementary material (see text). aChromosome. The segment location cytoband was derived from that of the first mapped gene within the segment. bSegment Start/End: chromosomal coordinates for each segment. cSignificantly over-/underexpressed genes as marked in the TRAM results. dCytoband not available in Gene was derived from the UCSC Genome Browser (http://genome-euro.ucsc.edu/cgi-bin/hgGateway)
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BMC Genomics

ISSN: 1471-2164

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