SZGR2

Summary ?

GeneID	6397
Symbol	SEC14L1
Synonyms	PRELID4A\|SEC14L
Description	SEC14 like lipid binding 1
Reference	MIM:601504\|HGNC:HGNC:10698\|Ensembl:ENSG00000129657\|HPRD:03295\|Vega:OTTHUMG00000177311
Gene type	protein-coding
Map location	17q25.2
Pascal p-value	0.288
Sherlock p-value	0.611
Fetal beta	-0.798
DMG	3 (# studies)
eGene	Myers' cis & trans
Support	CompositeSet Darnell FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Jaffe_2016	Genome-wide DNA methylation analysis	This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05.	7
DMG:Montano_2016	Genome-wide DNA methylation analysis	This dataset includes 172 replicated associations between CpGs with schizophrenia.	7
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).	7
Expression	Meta-analysis of gene expression	P value: 1.526

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg11186858	17	75096382	SEC14L1	4.93E-6	0.011	0.029	DMG:Montano_2016
cg11597902	17	75096239	SEC14L1	1.49E-5	0.01	0.054	DMG:Montano_2016
cg20610950	17	75096202	SEC14L1	7.93E-5	0.012	0.112	DMG:Montano_2016
cg26547236	17	75136326	SEC14L1	1.4E-8	-0.017	5.44E-6	DMG:Jaffe_2016
cg04452095	17	75315868	SEC14L1	7.817E-4	-4.44		DMG:vanEijk_2014
cg03330678	17	75316233	SEC14L1	5.18E-5	-4.793		DMG:vanEijk_2014
cg03330678	17	75316233	SEC14L1	4.57E-5	-5.707		DMG:vanEijk_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs11695174	chr2	9788314	SEC14L1	6397		0.2		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
ACIN1	0.93	0.92
LAS1L	0.92	0.92
RBM6	0.92	0.93
ANKZF1	0.92	0.92
RBM5	0.92	0.92
TRPV1	0.92	0.93
CLK2	0.91	0.92
MICAL1	0.91	0.91
FNBP4	0.91	0.91
ANO8	0.90	0.90

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.70	-0.79
B2M	-0.67	-0.73
AF347015.27	-0.67	-0.76
IFI27	-0.66	-0.74
MT-CO2	-0.66	-0.76
COPZ2	-0.65	-0.71
C5orf53	-0.64	-0.65
MT-CYB	-0.63	-0.72
HIGD1B	-0.63	-0.74
PSMB9	-0.63	-0.70

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005488	binding	TAS		8697811
GO:0005215	transporter activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006810	transport	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005794	Golgi apparatus	TAS		8697811
GO:0005622	intracellular	IEA		-
GO:0016020	membrane	TAS		8697811

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
TURASHVILI BREAST DUCTAL CARCINOMA VS DUCTAL NORMAL DN	198	110	All SZGR 2.0 genes in this pathway
WILCOX RESPONSE TO PROGESTERONE UP	152	90	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE DN	384	220	All SZGR 2.0 genes in this pathway
DITTMER PTHLH TARGETS UP	112	68	All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP	456	228	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 6HR DN	167	100	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
HAHTOLA MYCOSIS FUNGOIDES UP	19	15	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS DN	142	95	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 DN	153	100	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
LASTOWSKA NEUROBLASTOMA COPY NUMBER UP	181	108	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN	483	336	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS DN	366	238	All SZGR 2.0 genes in this pathway
THEILGAARD NEUTROPHIL AT SKIN WOUND DN	225	163	All SZGR 2.0 genes in this pathway
MCCLUNG COCAINE REWARD 5D	79	62	All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE DN	123	76	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN	287	208	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP	953	554	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP	783	442	All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 UNSTIMULATED	1229	713	All SZGR 2.0 genes in this pathway
STEIN ESRRA TARGETS DN	105	63	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR UP	430	288	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE DN	274	165	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL DN	216	143	All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A12	317	177	All SZGR 2.0 genes in this pathway
STEIN ESRRA TARGETS	535	325	All SZGR 2.0 genes in this pathway
ACOSTA PROLIFERATION INDEPENDENT MYC TARGETS DN	116	74	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 DN	918	550	All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS UP	682	433	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS DN	211	119	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
let-7/98	453	459	1A	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-190	419	425	1A	hsa-miR-190	UGAUAUGUUUGAUAUAUUAGGU
miR-208	383	389	1A	hsa-miR-208	AUAAGACGAGCAAAAAGCUUGU
miR-218	178	184	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-23	516	523	1A,m8	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	516	523	1A,m8	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-323	516	522	1A	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-499	383	389	1A	hsa-miR-499	UUAAGACUUGCAGUGAUGUUUAA

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: SEC14L1