Deciphering modular and dynamic behaviors of transcriptional networks

Zhan, Ming

doi:10.1007/s11568-007-9004-7

The HUGO Journal

Official Journal of the Human Genome Organisation

Table 2 Probabilities of the network behavior transition by serial interventions on the genes in the ABL-BCR pathway of human

From: Deciphering modular and dynamic behaviors of transcriptional networks

Gene	Transcriptional intervention	Transition probability
(A) Transition from normal to CML states by single-gene intervention^a
BCR	0⇒−1⇒1	0.00639
(B) Transition from CML to normal states by single-gene intervention^a
ABL1	1⇒0⇒−1	0.000299
(C) Transition from the normal to CML states by double-gene intervention^b
BCR ABL1	0 −1⇒1 1⇒1 1	0.0109
BCR BAD	0 1⇒−1 0⇒1 0	0.00639
BCR MYC	0 −1⇒−1 0⇒1 0	0.00639
BCR BAD	0 1⇒−1 −1⇒1 0	0.00639
BCR MYC	0 −1⇒−1 1⇒1 0	0.00639
BCR STAT5A	0 1⇒−1 −1⇒1 1	0.00639
BCR STAT5A	0 1⇒−1 0⇒1 1	0.00639
BCR STAT1	0 0⇒−1 1⇒1 0	0.00639
BCR STAT1	0 0⇒−1 −1⇒1 0	0.00639
BCR CRKL	0 −1⇒−1 1⇒1 0	0.00539
BCR CRKL	0 −1⇒−1 0⇒1 0	0.00399
BCR PIK3CG	0 −1⇒−1 0⇒1 −1	0.00384
BCR JAK2	0 0⇒ −1 1⇒1 0	0.00224
BCR AKT1	0 0⇒−1 −1⇒1 0	0.00107
(D) Transition from the CML to normal states by double-gene intervention^b
ABL1 AKT1	1 0⇒0 1⇒−1 0	0.00185
ABL1 AKT1	1 0⇒0 −1⇒−1 0	0.00179
BCR ABL1	1 1⇒0 −1⇒0 −1	0.00111
(E) Transition from normal to CML states by triple-gene intervention^c
BCR ABL1 BAD	0 −1 1⇒1 1 0⇒1 1 0	0.010936
BCR ABL1 MYC	0 −1 −1⇒1 1 0⇒1 1 0	0.010936
BCR ABL1 BAD	0 −1 1⇒1 1 −1⇒1 1 0	0.010933
BCR ABL1 MYC	0 −1 −1⇒1 1 1⇒1 1 0	0.010933
BCR ABL1 STAT5A	0 −1 1⇒1 1 0⇒1 1 1	0.010933
BCR ABL1 STAT5A	0 −1 1⇒1 1 −1⇒1 1 1	0.010933
BCR ABL1 STAT1	0 −1 0⇒1 1 −1⇒1 1 0	0.010933
BCR ABL1 STAT1	0 −1 0⇒1 1 1⇒1 1 0	0.010933
(F) Transition from CML to normal states by triple-gene intervention^d
BCR ABL1 AKT1	1 1 0⇒0 −1 1⇒0 −1 0	0.00684
BCR ABL1 AKT1	1 1 0⇒0 −1 −1⇒0 −1 0	0.00662
ABL1 CRKL AKT1	1 0 0⇒0 −1 1⇒−1 −1 0	0.00297
ABL1 CRKL AKT1	1 0 0⇒0 −1 −1⇒−1 −1 0	0.00288
BCR ABL1 AKT1	1 1 0⇒−1 −1 1⇒0 −1 0	0.00274
BCR ABL1 AKT1	1 1 0⇒−1 −1 −1⇒0 −1 0	0.00265
ABL1 CRKL AKT1	1 0 0⇒0 1 1⇒−1 −1 0	0.00250
ABL1 CRKL AKT1	1 0 0⇒0 1 −1⇒−1 −1 0	0.00242

The gene expression profile of each state is presented as: initial state (e.g., normal state) ⇒ state after intervened ⇒ end state (e.g., disease state). Transcriptional intervention is presented as: initial state (e.g., normal state) ⇒ state after intervened ⇒ end state (e.g., disease state). In each state, expression levels of each gene are presented by ternary values
^aProbability cutoff 1E-4
^bProbability cutoff 1E-3
^cProbability cutoff 1E-2
^dProbability cutoff 2E-3

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