Table 1

Gene co-expression networks nomenclature and number of differentially expressed (DE) genes (nodes) used to construct them
Networks built with DE genes from dose comparisons with control at time
Dose Comparison at Time No.DE genes Network name (samples used to build net)
Dose 0–10 at T0 810 networkA (samples with dose 0 and 10 cGy at T0)
Dose 0–100 at T0 525 networkB (samples with dose 0 and 100 cGy at T0)
Dose 0–10 at T3 1008 networkC (samples with dose 0 and 10 cGy at T3)
Dose 0–100 at T3 1000 networkD (samples with dose 0 and 100 cGy at T3)
Dose 0–10 at T8 203 networkE (samples with dose 0 and 10 cGy at T8)
Dose 0–100 at T8 972 networkF (samples with dose 0 and 100 cGy at T8)
Dose 0–10 at T24 702 networkG (samples with dose 0 and 10 cGy at T24)
Dose 0–100 at T24 953 networkH (samples with dose 0 and 100 cGy at T24)
Networks built with common DE genes from two dose comparisons with control at time
Dose Comparison at Time No.common DE genes Network name (samples used to build net)
Dose 0–10 at T0 199 netAB1 (samples with dose 0 and 10 cGy at T0)
Dose 0–100 at T0 netAB2 (samples with dose 0 and 100 cGy at T0)
Dose 0–10 at T3 503 netCD1 (samples with dose 0 and 10 cGy at T3)
Dose 0–100 at T3 netCD2 (samples with dose 0 and 100 cGy at T3)
Dose 0–10 at T8 86 netEF1 (samples with dose 0 and 10 cGy at T8)
Dose 0–100 at T8 netEF2 (samples with dose 0 and 100 cGy at T8)
Dose 0–10 at T24 482 netGH1 (samples with dose 0 and 10 cGy at T24)
Dose 0–100 at T24 netGH2 (samples with dose 0 and 100 cGy at T24)

In networkA (number of nodes = 810) inter-gene correlation was computed for samples exposed to dose 0 and 10 cGy at time 0. In networkB (number of nodes = 525) inter-gene correlation was computed for samples exposed to dose 0 and 100 cGy at time 0. In networkC inter-gene correlation was computed for samples exposed to dose 0 and 10 cGy at time 3. In networkD inter-gene correlation was computed for samples exposed to dose 0 and 100 cGy at time 3. Same protocol for networks networkE,networkF, networkG and networkH. In netAB1 (number of nodes = 199) inter-gene correlation was computed for samples exposed to dose 0 and 10 cGy at time 0. Same protocol for networks netAB2, netCD1, netCD2, netEF1, netEF2, netGH1 and netGH2. The main difference between networks in the top half and the bottom half of the table is the nodes/DE genes used to construct them.

Ray et al.

Ray et al. BMC Genomics 2012 13:190   doi:10.1186/1471-2164-13-190

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