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. 2014 Dec 5;7:63. doi: 10.1186/s12920-014-0063-z

Table 6.

Genomic segments significantly over- or under-expressed

a) DS AMKL vs. TMD
Chr a and location Segment start b Segment end b 'A'/'C' ratio q-value Genes in the segment c
Over-expressed segments
chr2 2q31.3 182,000,001 182,500,000 2.20 0.00045 ITGA4 + Hs.660611- Hs.658786+ CERKL+ Hs.72981+
chr8 8q21.3 91,750,001 92,250,000 1.40 0.00051 NECAB1 + Hs.743640+ LOC100127983+ TMEM55A+ LOC100506365- OTUD6B+ LRRC69+
b) TMD vs. normal MK
Chr and location Segment start Segment end 'C'/'D' ratio q-value Genes in the segment
Over-expressed segments
chr3 3p26.2 3,500,001 4,000,000 28.00 0.00006 Hs.241414+ d Hs.587205+ LRRN1 + Hs.128128+
chr15 15q26.2 96,750,001 97,250,000 19.86 0.00000 Hs.677040+ d Hs.661950+ d NR2F2-AS1 + NR2F2- Hs.592015+
c) TMD vs. normal CB MK
Chr and location Segment start Segment end 'C'/'E' ratio q-value Genes in the segment
chr3
3q22.1
130,000,001 130,500,000 75.97 0.00015 COL6A5 + COL6A6 + Hs.596709+ Hs.596805+ PIK3R4-

Data refer to the following comparisons: a) DS AMKL (pool 'A') vs. TMD (pool 'C'); b) TMD (pool 'C') vs. normal MK (pool 'D'); c) TMD (pool 'C') vs. normal CB MK (pool 'E'). Analysis was performed using default parameters (see Methods section). Segments are sorted by increasing 'A'/'C' ratio in a), 'C'/'D' ratio in b) and 'C'/'E' ratio in c). 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. Some segments are not shown for simplicity because they are over-lapping with those highlighted in one of the listed regions. The complete results for this model are available as additional material on line.

aChr: chromosome. The segment location cytoband was derived from that of the first mapped gene within the segment.

bSegment Start/End: chromosomal coordinates for each segment.

cBold and '+': over-expressed gene; bold and '-': under-expressed gene; '+' or '-': gene expression value higher or lower than the median value, respectively.

dThis UniGene cluster contains EST with at least one Alu sequence, according to Repeat Masker [46]. For this reason, it can not be excluded that its over-expression is related to non-specific hybridization by Alu-containg probes.