SZGR2

Summary ?

GeneID	8766
Symbol	RAB11A
Synonyms	YL8
Description	RAB11A, member RAS oncogene family
Reference	MIM:605570\|HGNC:HGNC:9760\|Ensembl:ENSG00000103769\|HPRD:05715\|Vega:OTTHUMG00000133162
Gene type	protein-coding
Map location	15q22.31
Pascal p-value	0.442
Sherlock p-value	0.005
Fetal beta	0.472
DMG	1 (# studies)

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.	1
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.8396

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg23900535	15	66161693	RAB11A	2.14E-8	-0.008	7.26E-6	DMG:Jaffe_2016

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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0019905	syntaxin binding	NAS	Synap (GO term level: 5)	12145319
GO:0000166	nucleotide binding	IEA		-
GO:0003924	GTPase activity	NAS		11163216
GO:0005524	ATP binding	IEA		-
GO:0005525	GTP binding	IEA		-
GO:0005215	transporter activity	NAS		11163216
GO:0008134	transcription factor binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006355	regulation of transcription, DNA-dependent	IEA		-
GO:0007264	small GTPase mediated signal transduction	IEA		-
GO:0015031	protein transport	IEA		-
GO:0048227	plasma membrane to endosome transport	NAS		11163216
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0055038	recycling endosome membrane	IEA		-
GO:0005802	trans-Golgi network	IDA		15229288
GO:0005622	intracellular	IEA		-
GO:0005768	endosome	IEA		-
GO:0005886	plasma membrane	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
GDI2	FLJ16452 \| FLJ37352 \| RABGDIB	GDP dissociation inhibitor 2	-	HPRD,BioGRID	10512627
MYO5B	KIAA1119	myosin VB	-	HPRD,BioGRID	11408590 \|11495908
RAB11FIP1	DKFZp686E2214 \| FLJ22524 \| FLJ22622 \| MGC78448 \| NOEL1A \| RCP \| rab11-FIP1	RAB11 family interacting protein 1 (class I)	Affinity Capture-MS in vitro in vivo Reconstituted Complex Two-hybrid	BioGRID	11495908 \|11786538 \|17353931
RAB11FIP2	KIAA0941 \| Rab11-FIP2 \| nRip11	RAB11 family interacting protein 2 (class I)	-	HPRD	15304524
RAB11FIP2	KIAA0941 \| Rab11-FIP2 \| nRip11	RAB11 family interacting protein 2 (class I)	-	HPRD,BioGRID	11495908 \|11994279
RAB11FIP3	KIAA0665 \| Rab11-FIP3	RAB11 family interacting protein 3 (class II)	in vitro Two-hybrid	BioGRID	11495908
RAB11FIP3	KIAA0665 \| Rab11-FIP3	RAB11 family interacting protein 3 (class II)	-	HPRD	11481332
RAB11FIP4	FLJ00131 \| KIAA1821 \| MGC11316 \| MGC126566 \| RAB11-FIP4	RAB11 family interacting protein 4 (class II)	-	HPRD,BioGRID	12470645
RAB11FIP5	DKFZp434H018 \| GAF1 \| KIAA0857 \| RIP11 \| pp75	RAB11 family interacting protein 5 (class I)	Rab11 interacts with the carboxy terminus, including the coiled-coil region, of Gaf-1.	BIND	12554740
RAB11FIP5	DKFZp434H018 \| GAF1 \| KIAA0857 \| RIP11 \| pp75	RAB11 family interacting protein 5 (class I)	Affinity Capture-Western in vitro in vivo Reconstituted Complex Two-hybrid	BioGRID	11163216 \|11495908
RAB3IL1	GRAB	RAB3A interacting protein (rabin3)-like 1	Two-hybrid	BioGRID	16189514
SEC13	D3S1231E \| SEC13L1 \| SEC13R \| npp-20	SEC13 homolog (S. cerevisiae)	Two-hybrid	BioGRID	10747849
STX4	STX4A \| p35-2	syntaxin 4	-	HPRD	12435603
WDR44	DKFZp686L20145 \| MGC26781 \| RAB11BP \| RPH11	WD repeat domain 44	-	HPRD,BioGRID	10077598 \|10464283

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG ENDOCYTOSIS	183	132	All SZGR 2.0 genes in this pathway
KEGG VASOPRESSIN REGULATED WATER REABSORPTION	44	30	All SZGR 2.0 genes in this pathway
BIOCARTA RAB PATHWAY	12	8	All SZGR 2.0 genes in this pathway
PID NOTCH PATHWAY	59	49	All SZGR 2.0 genes in this pathway
PID TXA2PATHWAY	57	43	All SZGR 2.0 genes in this pathway
PID ARF6 DOWNSTREAM PATHWAY	15	14	All SZGR 2.0 genes in this pathway
PID IL8 CXCR2 PATHWAY	34	26	All SZGR 2.0 genes in this pathway
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES	413	270	All SZGR 2.0 genes in this pathway
REACTOME AQUAPORIN MEDIATED TRANSPORT	51	34	All SZGR 2.0 genes in this pathway
REACTOME REGULATION OF WATER BALANCE BY RENAL AQUAPORINS	44	30	All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN	634	384	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
GARGALOVIC RESPONSE TO OXIDIZED PHOSPHOLIPIDS RED DN	25	19	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 MUTATED SIGNATURE 1 DN	126	86	All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN	281	186	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 DN	162	116	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 UP	120	73	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA DN	394	258	All SZGR 2.0 genes in this pathway
OUELLET CULTURED OVARIAN CANCER INVASIVE VS LMP UP	69	40	All SZGR 2.0 genes in this pathway
SEIDEN MET SIGNALING	19	16	All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER	747	453	All SZGR 2.0 genes in this pathway
TOMLINS PROSTATE CANCER UP	40	27	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR UP	487	286	All SZGR 2.0 genes in this pathway
BENPORATH MYC MAX TARGETS	775	494	All SZGR 2.0 genes in this pathway
FLECHNER PBL KIDNEY TRANSPLANT OK VS DONOR DN	41	30	All SZGR 2.0 genes in this pathway
SMITH TERT TARGETS DN	87	69	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP	555	346	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
JIANG VHL TARGETS	138	91	All SZGR 2.0 genes in this pathway
TAKAO RESPONSE TO UVB RADIATION DN	98	67	All SZGR 2.0 genes in this pathway
GENTILE UV RESPONSE CLUSTER D7	40	21	All SZGR 2.0 genes in this pathway
GENTILE UV HIGH DOSE DN	312	203	All SZGR 2.0 genes in this pathway
JOSEPH RESPONSE TO SODIUM BUTYRATE UP	31	21	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 5	482	296	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN DN	249	165	All SZGR 2.0 genes in this pathway
BONOME OVARIAN CANCER SURVIVAL OPTIMAL DEBULKING	246	152	All SZGR 2.0 genes in this pathway
GOLDRATH ANTIGEN RESPONSE	346	192	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP	518	299	All SZGR 2.0 genes in this pathway
KYNG WERNER SYNDROM AND NORMAL AGING UP	93	62	All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC	1103	714	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION UP	271	165	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-124.1	517	524	1A,m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	517	523	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	517	523	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-141/200a	863	869	1A	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	863	869	1A	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-142-3p	1167	1173	1A	hsa-miR-142-3p	UGUAGUGUUUCCUACUUUAUGGA
miR-142-5p	146	152	1A	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-181	226	232	m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-21	363	370	1A,m8	hsa-miR-21^brain	UAGCUUAUCAGACUGAUGUUGA
miR-21	363	370	1A,m8	hsa-miR-590	GAGCUUAUUCAUAAAAGUGCAG
miR-216	51	57	m8	hsa-miR-216	UAAUCUCAGCUGGCAACUGUG
miR-26	308	314	1A	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	308	314	1A	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-30-5p	250	256	m8	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-542-3p	273	279	m8	hsa-miR-542-3p	UGUGACAGAUUGAUAACUGAAA
miR-543	227	233	m8	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-93.hd/291-3p/294/295/302/372/373/520	1258	1265	1A,m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU

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: RAB11A