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.