SZGR2

Summary ?

GeneID	27086
Symbol	FOXP1
Synonyms	12CC4\|HSPC215\|MFH\|QRF1\|hFKH1B
Description	forkhead box P1
Reference	MIM:605515\|HGNC:HGNC:3823\|Ensembl:ENSG00000114861\|HPRD:18518\|Vega:OTTHUMG00000158803
Gene type	protein-coding
Map location	3p14.1
Pascal p-value	5.045E-9
Sherlock p-value	0.836
Fetal beta	0.06
DMG	1 (# studies)
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Nishioka_2013	Genome-wide DNA methylation analysis	The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls.	1
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.04047
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.04359
Expression	Meta-analysis of gene expression	P value: 1.87
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg24980458	3	71632677	FOXP1		-0.02	0.41	DMG:Nishioka_2013

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs2033050	chr7	134933767	FOXP1	27086		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
MRTO4	0.79	0.79
NARFL	0.78	0.78
CDK10	0.78	0.79
NCAPH2	0.77	0.80
RAB24	0.77	0.77
PICK1	0.77	0.76
TTLL3	0.77	0.77
STK25	0.76	0.76
RING1	0.76	0.77
PNKP	0.76	0.75

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.2	-0.64	-0.59
AF347015.8	-0.63	-0.58
AF347015.15	-0.62	-0.59
AF347015.31	-0.62	-0.58
MT-CYB	-0.62	-0.59
AF347015.27	-0.61	-0.59
MT-ATP8	-0.61	-0.63
AF347015.26	-0.60	-0.59
MT-CO2	-0.60	-0.54
AF347015.33	-0.59	-0.56

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0003700	transcription factor activity	IEA		-
GO:0003705	RNA polymerase II transcription factor activity, enhancer binding	IEA		-
GO:0008270	zinc ion binding	IEA		-
GO:0016566	specific transcriptional repressor activity	IEA		-
GO:0042803	protein homodimerization activity	IEA		-
GO:0046872	metal ion binding	IEA		-
GO:0046982	protein heterodimerization activity	IEA		-
GO:0043565	sequence-specific DNA binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007519	skeletal muscle development	IEA	neuron (GO term level: 8)	-
GO:0000122	negative regulation of transcription from RNA polymerase II promoter	IEA		-
GO:0002639	positive regulation of immunoglobulin production	IEA		-
GO:0002053	positive regulation of mesenchymal cell proliferation	IEA		-
GO:0002329	pre-B cell differentiation	IEA		-
GO:0055007	cardiac muscle cell differentiation	IEA		-
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0009790	embryonic development	IEA		-
GO:0007507	heart development	IEA		-
GO:0016481	negative regulation of transcription	IEA		-
GO:0033152	immunoglobulin V(D)J recombination	IEA		-
GO:0030324	lung development	IEA		-
GO:0048745	smooth muscle development	IEA		-
GO:0050679	positive regulation of epithelial cell proliferation	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005622	intracellular	IEA		-
GO:0005634	nucleus	IEA		-
GO:0005730	nucleolus	IDA		18029348

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
PICCALUGA ANGIOIMMUNOBLASTIC LYMPHOMA DN	136	86	All SZGR 2.0 genes in this pathway
RODRIGUES DCC TARGETS DN	121	84	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA UP	1821	933	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN	805	505	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN	537	339	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS CDC25 DN	51	35	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS DN	142	95	All SZGR 2.0 genes in this pathway
MARKEY RB1 CHRONIC LOF UP	115	78	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN	770	415	All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS UP	169	127	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER DN	514	319	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS DN	411	249	All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS	734	436	All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION UP	195	138	All SZGR 2.0 genes in this pathway
MCCLUNG CREB1 TARGETS DN	57	39	All SZGR 2.0 genes in this pathway
HAN JNK SINGALING UP	35	21	All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS DN	142	94	All SZGR 2.0 genes in this pathway
SAFFORD T LYMPHOCYTE ANERGY	87	54	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 5	482	296	All SZGR 2.0 genes in this pathway
ZHENG BOUND BY FOXP3	491	310	All SZGR 2.0 genes in this pathway
ZHENG FOXP3 TARGETS IN T LYMPHOCYTE DN	37	29	All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN	409	268	All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS UP	673	430	All SZGR 2.0 genes in this pathway
MARTINEZ TP53 TARGETS DN	593	372	All SZGR 2.0 genes in this pathway
MARTINEZ RB1 AND TP53 TARGETS DN	591	366	All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN	940	425	All SZGR 2.0 genes in this pathway
COLINA TARGETS OF 4EBP1 AND 4EBP2	356	214	All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK	1210	725	All SZGR 2.0 genes in this pathway
MIKKELSEN DEDIFFERENTIATED STATE DN	7	7	All SZGR 2.0 genes in this pathway
MARSON FOXP3 TARGETS DN	54	38	All SZGR 2.0 genes in this pathway
ASGHARZADEH NEUROBLASTOMA POOR SURVIVAL DN	46	30	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 0	76	54	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN	1972	1213	All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN	315	215	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG BOUND 8D	658	397	All SZGR 2.0 genes in this pathway
ACEVEDO FGFR1 TARGETS IN PROSTATE CANCER MODEL UP	289	184	All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP	489	314	All SZGR 2.0 genes in this pathway
ZWANG EGF PERSISTENTLY DN	61	36	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	773	779	1A	hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
				hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
				hsa-miR-1	UGGAAUGUAAAGAAGUAUGUA
				hsa-miR-206^SZ	UGGAAUGUAAGGAAGUGUGUGG
				hsa-miR-613	AGGAAUGUUCCUUCUUUGCC
miR-132/212	2697	2703	1A	hsa-miR-212^SZ	UAACAGUCUCCAGUCACGGCC
miR-132/212	2697	2703	1A	hsa-miR-132^brain	UAACAGUCUACAGCCAUGGUCG
miR-139	2808	2814	m8	hsa-miR-139^brain	UCUACAGUGCACGUGUCU
miR-141/200a	282	288	m8	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	282	288	m8	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-150	172	178	m8	hsa-miR-150	UCUCCCAACCCUUGUACCAGUG
miR-181	705	711	m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-183	153	159	m8	hsa-miR-183	UAUGGCACUGGUAGAAUUCACUG
miR-19	439	446	1A,m8	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	439	446	1A,m8	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-191	823	829	m8	hsa-miR-191^brain	CAACGGAAUCCCAAAAGCAGCU
miR-22	2523	2529	m8	hsa-miR-22^brain	AAGCUGCCAGUUGAAGAACUGU
miR-221/222	2810	2816	1A	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	2810	2816	1A	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-30-3p	2886	2893	1A,m8	hsa-miR-30a-3p	CUUUCAGUCGGAUGUUUGCAGC
miR-30-3p	2886	2893	1A,m8	hsa-miR-30e-3p	CUUUCAGUCGGAUGUUUACAGC
miR-324-3p	71	77	1A	hsa-miR-324-3p	CCACUGCCCCAGGUGCUGCUGG
miR-329	540	546	1A	hsa-miR-329^brain	AACACACCUGGUUAACCUCUUU
miR-33	1356	1362	1A	hsa-miR-33	GUGCAUUGUAGUUGCAUUG
miR-33	1356	1362	1A	hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
miR-34/449	465	471	m8	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
				hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-34b	466	472	m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-34b	466	472	m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-369-3p	725	731	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	725	731	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-409-3p	819	825	m8	hsa-miR-409-3p	CGAAUGUUGCUCGGUGAACCCCU
miR-543	706	713	1A,m8	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-9	1730	1737	1A,m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-9	1730	1737	1A,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: FOXP1