Table 4.
PPARs and other regulatory partners were automatically proposed from experimental lists of PPARA gene targets
|
Input list 1
a
|
Input list 2
a
|
Input list 1
a
|
Input list 2
a
|
||||
|---|---|---|---|---|---|---|---|
|
Score: coverage
b
|
Score: specificity
b
|
||||||
| RXR | RXR | ||||||
| RXRA: PPARG |
[4-29]c |
RXRA |
[2-20] |
RXRA: PXR-isoform1A |
[1] |
RXRA: PPARA |
[4] |
| RXRA: PPARA |
[4-29] |
RXRA: VDR |
[2-20] |
RXR: VDR |
[3] |
RXRA: PPARD |
[5-8] |
| RXRA: PPARD |
[4-29] |
|
|
RXRA: PPARD |
[4] |
RXRG: PPARA |
[5-8] |
| RXRG: PPARA |
[4-29] |
|
|
RXRA: PPARG |
[14] |
RXRG: PPARD |
[5-8] |
| RXRG: PPARD |
[4-29] |
|
|
|
|
RXRA: PPARG |
[9,10] |
| RXRG: PPARG |
[4-29] |
|
|
|
|
RXRG: PPARG |
[9,10] |
| RXRG: PPARG |
[4-29] |
|
|
|
|
|
|
|
VDR |
VDR |
||||||
| VDR |
[30-2223] |
VDR |
[2-20] |
VDR: RXRA |
[3] |
|
|
| VDR: RXRA |
[30-2223] |
VDR: RXRA |
[2-20] |
|
|
|
|
| VDR: calcitriol |
[30-2223] |
|
|
|
|
|
|
| VDR: calcitriol: 9-cis-retinoic acid: RXRA |
[30-2223] |
|
|
|
|
|
|
| VDR: BLM |
[30-2223] |
|
|
|
|
|
|
|
PPARA |
PPARA |
||||||
| PPARA: RXRA |
[4-29] |
PPARA |
[21-1702] |
PPARA: RXRA |
[2] |
PPARA: RXRA |
[4] |
| PPARA: RXRG |
[4-29] |
PPARA: RXRA |
[21-1702] |
|
|
|
|
|
PPARG |
PPARG |
||||||
| PPARG: RXRA |
[4-29] |
PPARG: abietic acid |
[21-1702] |
PPARG: RXRA |
[14] |
PPARG: RXRA |
[9,10] |
| PPARG: RXRG |
[4-29] |
PPARG: 15d-PGJ2 |
[21-1702] |
|
|
PPARG: RXRG |
[9,10] |
| |
|
PPARG: azPC |
[21-1702] |
|
|
PPARG |
[12] |
|
PPARD |
PPARD |
||||||
| PPARD: RXRA | [4-29] | PPARD | [21-1702] | PPARD: RXRA | [4] | PPARD: RXR | [5-8] |
aDetailed lists are provided in Additional file 1: Table S1, with i) list 1 including 250 regulated genes identified as controlled by PPARA from a literature review [20] and ii) list 2 including 136 differentially expressed genes in response to PPARA agonists in cell culture [21].
bRegulatory candidates of these lists were elicited by an automatic algorithm based on encyclopedic information extracted from the TRANSPATH database and modeled as a causality graph. The candidates were scored for coverage (i.e., the number of targets regulated by a given candidate) or for specificity (i.e., a tradeoff between the number of regulated targets and the total number of regulated molecules) and the first 50th candidates having the highest scores were retained.
cThe range [Ni-Nj] indicated that the genes or the protein complex in which they participated had the same score as a set of Nj- Ni+1 molecules. When a molecule or a complex appeared more than once, only its best position was shown.