Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks

BMC Genomics

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.

ISSN: 1471-2164