Table 4.
Genomic segments significantly over- or under-expressed
| a) DS AMKL vs. normal CB MK | |||||
| Chr and location a | Segment start b | Segment end b | 'A'/'E' ratio | q-value | Genes in the segment c |
| Over-expressed segments | |||||
| chr3 3q22.1 | 130,000,001 | 130,500,000 | 80.36 | 0.00015 | COL6A5 + COL6A6 + Hs.596709+ Hs.596805+ PIK3R4- |
| Under-expressed segments | |||||
| chr7 7q11.23 | 77,000,001 | 77,500,000 | 0.48 | 0.00117 | GSAP - PTPN12 - LOC101059910- RSBN1L-AS1- RSBN1L- Hs.594486- Hs.720279- TMEM60- PHTF2- |
| chr4 4q12-q21 | 74,750,001 | 75,250,000 | 0.37 | 0.00119 | PF4 - PPBP - CXCL5- CXCL3 - CXCL2- MTHFD2L- Hs.662627- EREG- |
| chr4 4q32.1 | 156,250,001 | 156,750,000 | 0.12 | 0.00000 | MAP9 - GUCY1A3 - Hs.612374 - GUCY1B3 - |
| b) Non-DS AMKL vs. normal CB MK | |||||
| Chr and location | Segment start | Segment end | 'B'/'E' ratio | q-value | Genes in the segment |
| Over-expressed segments | |||||
| chr3 3q22.1 | 130,000,001 | 130,500,000 | 116.13 | 0.00030 | COL6A5 + COL6A6 + Hs.596709+ Hs.596805+ PIK3R4- |
| chr11 11p15 | 6,750,001 | 7,250,000 | 50.98 | 0.00117 | OR6A2+ OR10A5 + OR10A4 + ZNF215- ZNF214- Hs.445849+ NLRP14+ RBMXL2- LOC100506238+ |
| Under-expressed segments | |||||
| chr4 4q12-q21 | 74,750,001 | 75,250,000 | 0.42 | 0.00003 | PF4 - PPBP - CXCL5 - CXCL3 - CXCL2- MTHFD2L- Hs.662627- EREG- |
Data refer to the following comparisons: a) DS AMKL (pool 'A') vs. normal CB MK (pool 'E'); b) non-DS AMKL (pool 'B') vs. normal CB MK (pool 'E'). Analysis was performed using default parameters (see Methods section). Segments are sorted by increasing 'A'/'E' ratio in a), 'B'/'E' ratio in b). 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 on line additional material.
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.