Table 6.

The list of 25 most relevant pathways sorted by P value.

S.·no	Pathway name	Entities found	Ratio	P value	FDRa	Reactions found	Ratio
1	TFAP2 (AP-2) family regulates transcription of growth factors and their receptors	4/21	0.001	2.57E-08	6.88E-06	4/18	0.001
2	Potential therapeutics for SARS	5/84	0.006	0.000000122	0.0000163	6/32	0.002
3	SARS-CoV infections	6/203	0.014	0.000000338	0.0000301	9/254	0.019
4	Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors	4/52	0.004	9.37e-07	6.28e-05	4/44	0.003
5	Trafficking and processing of endosomal TLR	3/16	0.001	1.75e-06	9.29e-05	2/7	5.21e-04
6	Infectious disease	9/1343	0.092	0.0000516	0.002	16/750	0.056
7	VEGF ligand-receptor interactions	2/8	0.000551	0.0000633	0.002	3/4	0.000298
8	VEGF binds to VEGFR leading to receptor dimerization	2/8	5.51e-04	6.33e-05	0.002	2/3	2.23e-04
9	RUNX1 regulates transcription of genes involved in differentiation of keratinocytes	2/11	7.57e-04	1.19e-04	0.003	1/8	5.96e-04
10	Assembly of collagen fibrils and other multimeric structures	3/67	0.005	1.23e-04	0.003	1/26	0.002
11	Toll-like receptor cascades	4/188	0.013	0.000141	0.003	14/185	0.014
12	Disease	11/2360	0.163	0.000148	0.003	99/1591	0.119
13	Generic transcription pathway	9/1555	0.107	0.000163	0.003	17/824	0.061
14	Interleukin-4 and interleukin-13 signaling	4/211	0.015	2.19e-04	0.004	2/47	0.004
15	Regulation of gene expression by hypoxia-inducible factor	2/15	0.001	2.21e-04	0.004	1/7	5.21e-04
16	RNA polymerase II transcription	9/1694	0.117	0.000314	0.004	17/885	0.066
17	ERBB2 activates PTK6 signaling	2/18	0.001	0.000318	0.004	2/2	0.000149
18	ERBB2 regulates cell motility	2/19	0.001	0.000354	0.005	2/2	0.000149
19	Collagen formation	3/104	0.007	0.000444	0.006	1/77	0.006
20	PI3K events in ERBB2 signaling	2/22	0.002	0.000473	0.006	5/7	0.000521
21	Gene expression (transcription)	9/1855	0.128	0.000622	0.007	23/1000	0.074
22	Signaling by VEGF	3/137	0.009	0.000983	0.011	49/86	0.006
23	Signaling by ERBB2 KD Mutants	2/35	0.002	0.001	0.011	15/17	0.001
24	MHC class II antigen presentation	3/148	0.01	0.001	0.011	3/26	0.002
25	Degradation of the extracellular matrix	3/148	0.01	0.001	0.011	6/105	0.008

^aFalse discovery rate.