SZGR2

Summary ?

GeneID	5725
Symbol	PTBP1
Synonyms	HNRNP-I\|HNRNPI\|HNRPI\|PTB\|PTB-1\|PTB-T\|PTB2\|PTB3\|PTB4\|pPTB
Description	polypyrimidine tract binding protein 1
Reference	MIM:600693\|HGNC:HGNC:9583\|Ensembl:ENSG00000011304\|HPRD:02823\|Vega:OTTHUMG00000181789
Gene type	protein-coding
Map location	19p13.3
Pascal p-value	0.276
Sherlock p-value	0.002
Fetal beta	0.945
DMG	2 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:vanEijk_2014	Genome-wide DNA methylation analysis	This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250).	6
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	6
Expression	Meta-analysis of gene expression	P value: 1.41

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg17357561	19	807322	PTBP1	3.767E-4	0.458	0.043	DMG:Wockner_2014
cg07073964	19	698371	PTBP1	5.303E-4	2.907		DMG:vanEijk_2014
cg17823175	19	828170	PTBP1	1.157E-4	2.471		DMG:vanEijk_2014
cg07239938	19	852813	PTBP1	4.209E-4	2.06		DMG:vanEijk_2014
cg09134726	19	841082	PTBP1	4.309E-4	2.012		DMG:vanEijk_2014
cg18084554	19	929046	PTBP1	1.745E-4	1.976		DMG:vanEijk_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs4436485	chr10	103245360	PTBP1	5725		0.19		trans

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
HNRNPH3	0.93	0.92
HNRNPA1P2	0.92	0.84
HDAC2	0.92	0.84
ANP32A	0.90	0.87
SUMO2	0.90	0.84
SMARCE1	0.90	0.88
HNRNPH1	0.89	0.86
CBX3	0.89	0.81
HAUS1	0.89	0.76
SET	0.89	0.84

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
TNFSF12	-0.62	-0.68
PTH1R	-0.61	-0.75
HLA-F	-0.61	-0.73
ALDOC	-0.60	-0.71
C5orf53	-0.60	-0.70
LDHD	-0.59	-0.70
AIFM3	-0.59	-0.71
FBXO2	-0.59	-0.66
TSC22D4	-0.59	-0.73
CA4	-0.58	-0.76

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000166	nucleotide binding	IEA		-
GO:0003676	nucleic acid binding	IEA		-
GO:0003723	RNA binding	IEA		-
GO:0005515	protein binding	IEA		-
GO:0005515	protein binding	IPI		10653975 \|16373488 \|16713569
GO:0008187	poly-pyrimidine tract binding	TAS		1906036
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0000398	nuclear mRNA splicing, via spliceosome	EXP		12226669
GO:0006397	mRNA processing	IEA		-
GO:0008380	RNA splicing	TAS		1906036
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005634	nucleus	IEA		-
GO:0005654	nucleoplasm	TAS		1641332
GO:0005730	nucleolus	TAS		1641332
GO:0030530	heterogeneous nuclear ribonucleoprotein complex	TAS		1641332

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME PROCESSING OF CAPPED INTRON CONTAINING PRE MRNA	140	77	All SZGR 2.0 genes in this pathway
REACTOME MRNA PROCESSING	161	86	All SZGR 2.0 genes in this pathway
REACTOME MRNA SPLICING	111	58	All SZGR 2.0 genes in this pathway
PARENT MTOR SIGNALING UP	567	375	All SZGR 2.0 genes in this pathway
LIU SOX4 TARGETS DN	309	191	All SZGR 2.0 genes in this pathway
PRAMOONJAGO SOX4 TARGETS DN	51	35	All SZGR 2.0 genes in this pathway
PUIFFE INVASION INHIBITED BY ASCITES UP	82	51	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER ZNF217 AMPLIFIED DN	335	193	All SZGR 2.0 genes in this pathway
GINESTIER BREAST CANCER 20Q13 AMPLIFICATION DN	180	101	All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP	456	228	All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS UP	457	269	All SZGR 2.0 genes in this pathway
SENESE HDAC1 AND HDAC2 TARGETS UP	238	144	All SZGR 2.0 genes in this pathway
SENESE HDAC2 TARGETS UP	114	66	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	All SZGR 2.0 genes in this pathway
WOOD EBV EBNA1 TARGETS UP	110	71	All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK	1652	1023	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN	1024	594	All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION DN	187	122	All SZGR 2.0 genes in this pathway
NING CHRONIC OBSTRUCTIVE PULMONARY DISEASE UP	157	105	All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE DN	245	154	All SZGR 2.0 genes in this pathway
SCHLINGEMANN SKIN CARCINOGENESIS TPA UP	42	24	All SZGR 2.0 genes in this pathway
JIANG VHL TARGETS	138	91	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 1	528	324	All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D DN	270	181	All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP	871	505	All SZGR 2.0 genes in this pathway
MELLMAN TUT1 TARGETS UP	19	11	All SZGR 2.0 genes in this pathway
JIANG HYPOXIA VIA VHL	34	24	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D	882	506	All SZGR 2.0 genes in this pathway
LOPEZ TRANSLATION VIA FN1 SIGNALING	35	21	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-1/206	45	51	1A	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-124.1	330	337	1A,m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	329	336	1A,m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	329	336	1A,m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-133	1031	1037	1A	hsa-miR-133a	UUGGUCCCCUUCAACCAGCUGU
miR-133	1031	1037	1A	hsa-miR-133b	UUGGUCCCCUUCAACCAGCUA
miR-153	687	693	1A	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-17-5p/20/93.mr/106/519.d	61	67	1A	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-200bc/429	1292	1298	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-326	94	100	1A	hsa-miR-326	CCUCUGGGCCCUUCCUCCAG
miR-448	686	693	1A,m8	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-9	1033	1039	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: PTBP1