A gene co-association network regulating gut microbial communities in a Duroc pig population

Reverter, Antonio; Ballester, Maria; Alexandre, Pamela A.; Mármol-Sánchez, Emilio; Dalmau, Antoni; Quintanilla, Raquel; Ramayo-Caldas, Yuliaxis

doi:10.1186/s40168-020-00994-8

Microbiome

Table 3 List of 47 key regulators revealed by the regulatory impact factors (RIF) analyses and their RIF1 and RIF2 scores, standardized association to the bacteria (Alpha_B) and protist (Alpha_P) diversity, phenotype of strongest association, pleiotropy, and number of connections in the PCIT-inferred network

From: A gene co-association network regulating gut microbial communities in a Duroc pig population

Regulator	RIF1	RIF2	Alpha_B	Alpha_P	Top_Association	Pleio	Conn
PRDM15	0.648	2.806	0.239	0.277	B_Treponema	10	942
HOXD12	1.342	2.536	− 0.667	− 0.624	B_Sphaerochaeta	1	910
ZNF514	0.045	2.607	− 2.938	0.310	B_Sphaerochaeta	5	889
KIAA1549	1.270	2.715	− 1.701	− 1.465	B_RFN20	3	812
KLF7	− 5.625	0.204	− 0.603	1.249	B_Bulleidia	2	807
CREB3L2	− 2.411	0.511	− 0.694	0.818	B_Sphaerochaeta	0	676
TFE3	− 0.127	2.144	1.045	− 0.216	B_Phascolarctobacterium	3	627
TBX15	2.506	1.414	− 0.373	− 1.229	B_Anaerovibrio	2	617
STAT1	− 1.464	2.285	− 1.043	0.370	B_Catenibacterium	5	607
PURG	1.542	2.173	− 1.320	0.338	B_Sphaerochaeta	2	595
ssc-mir-371	− 2.848	1.073	1.181	− 0.690	B_Roseburia	3	588
MTA3	0.390	2.097	− 0.952	− 0.107	P_Hypotrichomonas	2	556
OSR2	− 2.512	− 0.194	0.270	0.005	B_Lachnospira	3	473
DBX1	− 2.047	− 0.129	− 2.207	− 1.577	B_Peptococcus	4	468
UNCX	− 3.085	− 0.194	− 0.051	1.258	B_Desulfovibrio	1	426
MYEF2	− 0.754	− 2.657	1.215	2.430	B_Fibrobacter	4	391
GBX1	− 0.730	− 2.439	− 0.245	− 1.460	B_Campylobacter	2	380
ZNF134	− 2.419	0.128	− 0.572	1.686	B_Lactobacillus	2	370
ZNF606	− 2.419	0.128	− 0.572	1.686	B_Lactobacillus	2	370
SOX9	− 2.524	− 0.404	− 0.498	0.096	B_Anaerovibrio	0	284
KMT2C	− 0.311	− 2.260	− 0.628	− 0.811	B_Catenibacterium	3	281
RUNX2	− 3.631	− 1.878	− 0.206	− 1.776	B_Collinsella	3	273
ELF2	− 1.740	− 2.300	− 0.739	1.688	B_Mitsuokella	1	245
ZNF322	− 2.079	− 0.792	− 0.233	0.809	B_Collinsella	2	229
IRF2	− 0.764	− 2.656	− 0.697	− 1.697	B_Peptococcus	0	209
GTF2IRD1	2.117	0.660	− 1.421	0.132	B_Lachnospira	0	206
ZNF516	2.099	0.150	2.010	0.690	B_Fibrobacter	2	195
NFE2L2	− 2.077	− 0.227	0.705	− 0.051	B_Coprococcus	1	183
NCOR1	− 1.999	− 0.455	− 1.007	1.063	B_Coprococcus	2	165
KLF14	− 2.287	− 2.255	− 0.327	− 1.073	B_Sutterella	1	161
ZGLP1	2.029	− 0.491	0.577	0.729	B_Butyricicoccus	3	161
TCF4	− 2.497	− 1.382	0.280	− 0.333	B_Clostridium	1	150
TP73	− 2.788	− 0.275	0.633	− 1.082	B_Campylobacter	1	146
ZNF782	− 2.831	− 0.500	0.382	− 1.811	B_Desulfovibrio	0	132
SALL1	− 1.133	− 2.716	− 0.833	− 2.125	P_AlphaPROTO	2	131
TOX3	− 2.335	− 2.043	0.365	1.641	B_Lactobacillus	1	129
TRERF1	− 2.359	− 1.043	− 0.286	− 2.005	P_Neobalantidium	3	128
MECP2	− 2.059	− 0.864	0.536	− 0.591	B_Dorea	2	118
SMAD4	− 2.460	− 2.206	0.431	1.586	B_Catenibacterium	0	118
IKZF2	− 1.694	− 2.864	− 0.578	− 1.337	P_AlphaPROTO	0	117
ssc-mir-9817	− 1.841	− 2.175	2.358	2.135	B_RFN20	0	116
ZHX2	− 2.028	− 1.124	0.266	− 1.654	B_Desulfovibrio	1	109
ZNF282	− 1.657	− 2.258	0.954	1.573	B_Ruminococcus	0	85
BAZ2B	− 2.287	− 0.786	− 1.879	0.484	B_Clostridium	1	76
ssc-mir-29a	− 2.067	− 2.748	− 0.568	0.811	B_Lachnospira	2	62
NFATC3	− 2.132	− 2.525	0.270	0.442	B_Desulfovibrio	1	24
ZNF18	− 1.353	− 2.134	− 0.490	− 0.929	P_Neobalantidium	0	18

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