SZGR2

Summary ?

GeneID	9013
Symbol	TAF1C
Synonyms	MGC:39976\|SL1\|TAFI110\|TAFI95
Description	TATA-box binding protein associated factor, RNA polymerase I subunit C
Reference	MIM:604905\|HGNC:HGNC:11534\|Ensembl:ENSG00000103168\|HPRD:05364\|Vega:OTTHUMG00000176665
Gene type	protein-coding
Map location	16q24
Pascal p-value	0.743
Sherlock p-value	0.602
Fetal beta	0.983
eGene	Caudate basal ganglia Cerebellar Hemisphere Cerebellum Cortex Hippocampus Hypothalamus Nucleus accumbens basal ganglia Putamen basal ganglia Myers' cis & trans Meta
Support	CompositeSet

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
DNM:Fromer_2014	Whole Exome Sequencing analysis	This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
TAF1C	chr16	84213434	A	T	NM_001243156 NM_001243157 NM_001243158 NM_001243159 NM_001243160 NM_005679 NM_139353	p.549L>M p.243L>M p.243L>M p.166L>M p.98L>M p.575L>M p.481L>M	missense missense missense missense missense missense missense			Schizophrenia	DNM:Fromer_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs2081247	chr16	84221961	TAF1C	9013		0.1		cis
rs4489992	16	84206843	TAF1C	ENSG00000103168.12	1.398E-7	0	13826	gtex_brain_putamen_basal
rs3803643	16	84208032	TAF1C	ENSG00000103168.12	1.164E-8	0	12637	gtex_brain_putamen_basal
rs3803642	16	84208144	TAF1C	ENSG00000103168.12	1.122E-8	0	12525	gtex_brain_putamen_basal
rs12597741	16	84208667	TAF1C	ENSG00000103168.12	7.822E-8	0	12002	gtex_brain_putamen_basal
rs12597782	16	84208891	TAF1C	ENSG00000103168.12	8.053E-8	0	11778	gtex_brain_putamen_basal
rs34693209	16	84209138	TAF1C	ENSG00000103168.12	1.161E-8	0	11531	gtex_brain_putamen_basal
rs2288019	16	84209634	TAF1C	ENSG00000103168.12	5.422E-7	0	11035	gtex_brain_putamen_basal
rs3743637	16	84210172	TAF1C	ENSG00000103168.12	5.573E-7	0	10497	gtex_brain_putamen_basal
rs11149630	16	84210749	TAF1C	ENSG00000103168.12	5.452E-7	0	9920	gtex_brain_putamen_basal
rs8692	16	84211483	TAF1C	ENSG00000103168.12	5.184E-7	0	9186	gtex_brain_putamen_basal
rs2278043	16	84213965	TAF1C	ENSG00000103168.12	2.613E-9	0	6704	gtex_brain_putamen_basal
rs2303234	16	84214837	TAF1C	ENSG00000103168.12	1.415E-7	0	5832	gtex_brain_putamen_basal
rs3815814	16	84215314	TAF1C	ENSG00000103168.12	1.486E-7	0	5355	gtex_brain_putamen_basal

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
DDX49	0.95	0.95
PRMT1	0.93	0.95
EIF6	0.93	0.93
RUVBL2	0.92	0.94
CECR5	0.92	0.93
CFL1	0.91	0.92
ARMC6	0.91	0.94
EBP	0.91	0.93
ACTL6B	0.91	0.92
WDR74	0.91	0.93

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.33	-0.75	-0.83
AF347015.27	-0.75	-0.82
AF347015.8	-0.74	-0.82
MT-CO2	-0.74	-0.79
AF347015.31	-0.74	-0.80
MT-CYB	-0.74	-0.82
AF347015.15	-0.73	-0.82
AF347015.2	-0.72	-0.83
AF347015.26	-0.70	-0.82
AF347015.9	-0.67	-0.78

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME RNA POL I TRANSCRIPTION TERMINATION	22	12	All SZGR 2.0 genes in this pathway
REACTOME RNA POL I TRANSCRIPTION	89	64	All SZGR 2.0 genes in this pathway
REACTOME TRANSCRIPTION	210	127	All SZGR 2.0 genes in this pathway
REACTOME RNA POL I RNA POL III AND MITOCHONDRIAL TRANSCRIPTION	122	80	All SZGR 2.0 genes in this pathway
REACTOME RNA POL I TRANSCRIPTION INITIATION	25	14	All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN	335	193	All SZGR 2.0 genes in this pathway
RASHI RESPONSE TO IONIZING RADIATION 3	48	31	All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK	423	265	All SZGR 2.0 genes in this pathway
RICKMAN METASTASIS UP	344	180	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION UP	314	201	All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS DN	141	92	All SZGR 2.0 genes in this pathway
KYNG ENVIRONMENTAL STRESS RESPONSE NOT BY 4NQO IN OLD	13	10	All SZGR 2.0 genes in this pathway
KYNG ENVIRONMENTAL STRESS RESPONSE NOT BY 4NQO IN WS	40	26	All SZGR 2.0 genes in this pathway
KYNG ENVIRONMENTAL STRESS RESPONSE NOT BY GAMMA IN OLD	31	19	All SZGR 2.0 genes in this pathway
KYNG ENVIRONMENTAL STRESS RESPONSE NOT BY GAMMA IN WS	33	22	All SZGR 2.0 genes in this pathway
KYNG ENVIRONMENTAL STRESS RESPONSE NOT BY UV IN OLD	25	18	All SZGR 2.0 genes in this pathway
KYNG ENVIRONMENTAL STRESS RESPONSE NOT BY UV IN WS	12	9	All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE DN	195	135	All SZGR 2.0 genes in this pathway
KYNG ENVIRONMENTAL STRESS RESPONSE UP	56	41	All SZGR 2.0 genes in this pathway
MALONEY RESPONSE TO 17AAG UP	41	26	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN	668	419	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SURVIVAL DN	113	76	All SZGR 2.0 genes in this pathway

Gene Page: TAF1C