SZGR2

Summary ?

GeneID	214
Symbol	ALCAM
Synonyms	CD166\|MEMD
Description	activated leukocyte cell adhesion molecule
Reference	MIM:601662\|HGNC:HGNC:400\|Ensembl:ENSG00000170017\|HPRD:03389\|Vega:OTTHUMG00000159192
Gene type	protein-coding
Map location	3q13.1
Pascal p-value	0.022
Fetal beta	-0.886
eGene	Myers' cis & trans
Support	CELL ADHESION AND TRANSSYNAPTIC SIGNALING CompositeSet

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:PGCnp	Genome-wide Association Study	GWAS
DNM:Fromer_2014	Whole Exome Sequencing analysis	This study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.04047
GSMA_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.04359
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 4

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
ALCAM	chr3	105269062	A	T	NM_001243280 NM_001243281 NM_001627	p.489N>I p.489N>I p.489N>I	missense missense missense			Schizophrenia	DNM:Fromer_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs1578978	chr8	118196802	ALCAM	214		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
ALDH4A1	0.90	0.88
ACSBG1	0.90	0.85
HTRA1	0.88	0.86
GPR37L1	0.88	0.82
SELENBP1	0.88	0.79
PBXIP1	0.88	0.84
CHDH	0.88	0.84
ATP1A2	0.87	0.85
SFXN5	0.86	0.84
HEPACAM	0.86	0.83

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
FRG1	-0.56	-0.63
CCAR1	-0.56	-0.63
AC026786.2	-0.56	-0.64
RTF1	-0.55	-0.58
CYP2R1	-0.54	-0.62
PHF14	-0.54	-0.60
C11orf57	-0.53	-0.66
MED19	-0.53	-0.54
DUSP12	-0.53	-0.55
AC011491.1	-0.52	-0.57

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005102	receptor binding	TAS	Neurotransmitter (GO term level: 4)	7760007
GO:0005515	protein binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0008045	motor axon guidance	IEA	neuron, axon (GO term level: 14)	-
GO:0007155	cell adhesion	TAS		7760007
GO:0007165	signal transduction	TAS		7760007
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0043025	cell soma	IEA	axon, dendrite (GO term level: 4)	-
GO:0030424	axon	IEA	neuron, axon, Neurotransmitter (GO term level: 6)	-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0009897	external side of plasma membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG CELL ADHESION MOLECULES CAMS	134	93	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE	251	188	All SZGR 2.0 genes in this pathway
REACTOME L1CAM INTERACTIONS	86	62	All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 UP	408	247	All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP	579	346	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA UP	177	110	All SZGR 2.0 genes in this pathway
HUTTMANN B CLL POOR SURVIVAL DN	60	39	All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA DN	320	184	All SZGR 2.0 genes in this pathway
LIU VMYB TARGETS UP	127	78	All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER CLASSES UP	72	38	All SZGR 2.0 genes in this pathway
DOANE RESPONSE TO ANDROGEN UP	184	125	All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER ESR1 UP	112	72	All SZGR 2.0 genes in this pathway
WANG CLIM2 TARGETS UP	269	146	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS DN	536	332	All SZGR 2.0 genes in this pathway
LEE NEURAL CREST STEM CELL UP	146	99	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA DN	77	52	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
CHOW RASSF1 TARGETS UP	27	17	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA REVERSIBLY DN	29	21	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2A DN	141	84	All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA UP	536	340	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS LUMINAL	326	213	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS BASAL	330	217	All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER CLUSTER 7	20	11	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER DN	514	319	All SZGR 2.0 genes in this pathway
BORLAK LIVER CANCER EGF UP	57	41	All SZGR 2.0 genes in this pathway
WOOD EBV EBNA1 TARGETS DN	47	33	All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS DN	193	112	All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 2 DN	51	42	All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM1	229	137	All SZGR 2.0 genes in this pathway
WOTTON RUNX TARGETS DN	29	18	All SZGR 2.0 genes in this pathway
KOYAMA SEMA3B TARGETS DN	411	249	All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS	988	594	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 DN	517	309	All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215	893	528	All SZGR 2.0 genes in this pathway
SUNG METASTASIS STROMA UP	110	70	All SZGR 2.0 genes in this pathway
ROSS AML WITH PML RARA FUSION	77	62	All SZGR 2.0 genes in this pathway
UEDA PERIFERAL CLOCK	169	111	All SZGR 2.0 genes in this pathway
OKUMURA INFLAMMATORY RESPONSE LPS	183	115	All SZGR 2.0 genes in this pathway
NING CHRONIC OBSTRUCTIVE PULMONARY DISEASE UP	157	105	All SZGR 2.0 genes in this pathway
ABBUD LIF SIGNALING 1 DN	26	17	All SZGR 2.0 genes in this pathway
BROWN MYELOID CELL DEVELOPMENT UP	165	100	All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 1 UP	182	119	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP	214	133	All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C8	72	56	All SZGR 2.0 genes in this pathway
MARTINEZ RESPONSE TO TRABECTEDIN	50	32	All SZGR 2.0 genes in this pathway
WELCSH BRCA1 TARGETS UP	198	132	All SZGR 2.0 genes in this pathway
HEDENFALK BREAST CANCER BRCA1 VS BRCA2	163	113	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 11	57	40	All SZGR 2.0 genes in this pathway
XU GH1 AUTOCRINE TARGETS UP	268	157	All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 5	482	296	All SZGR 2.0 genes in this pathway
LEIN NEURON MARKERS	69	45	All SZGR 2.0 genes in this pathway
GAVIN FOXP3 TARGETS CLUSTER P4	100	62	All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN	220	147	All SZGR 2.0 genes in this pathway
FOSTER TOLERANT MACROPHAGE DN	409	268	All SZGR 2.0 genes in this pathway
KONDO PROSTATE CANCER HCP WITH H3K27ME3	97	72	All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION UP	282	183	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP	461	298	All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE UP	578	341	All SZGR 2.0 genes in this pathway
WORSCHECH TUMOR REJECTION UP	56	32	All SZGR 2.0 genes in this pathway
ACEVEDO NORMAL TISSUE ADJACENT TO LIVER TUMOR UP	174	96	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BRAIN DN	85	58	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER ERBB2 UP	147	83	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
ITO PTTG1 TARGETS UP	12	9	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP	425	298	All SZGR 2.0 genes in this pathway
LABBE WNT3A TARGETS UP	112	71	All SZGR 2.0 genes in this pathway
LABBE TGFB1 TARGETS DN	108	64	All SZGR 2.0 genes in this pathway
HUPER BREAST BASAL VS LUMINAL DN	59	44	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D DN	252	155	All SZGR 2.0 genes in this pathway
GOLDRATH ANTIGEN RESPONSE	346	192	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
WENDT COHESIN TARGETS UP	33	19	All SZGR 2.0 genes in this pathway
COULOUARN TEMPORAL TGFB1 SIGNATURE DN	138	99	All SZGR 2.0 genes in this pathway
YAMANAKA GLIOBLASTOMA SURVIVAL DN	9	7	All SZGR 2.0 genes in this pathway
KUROKAWA LIVER CANCER EARLY RECURRENCE UP	12	9	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA1 UP	101	66	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA3 UP	80	54	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA UP	207	143	All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA PR DN	44	34	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
KARLSSON TGFB1 TARGETS DN	207	139	All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP	682	440	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL	177	132	All SZGR 2.0 genes in this pathway
HIRSCH CELLULAR TRANSFORMATION SIGNATURE DN	103	67	All SZGR 2.0 genes in this pathway
WANG RESPONSE TO GSK3 INHIBITOR SB216763 UP	397	206	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 6HR DN	91	56	All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN	505	328	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP	504	321	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 2 DN	336	211	All SZGR 2.0 genes in this pathway
ISSAEVA MLL2 TARGETS	62	35	All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP	745	475	All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3	824	528	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 1HR DN	6	5	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 PARTIAL	160	106	All SZGR 2.0 genes in this pathway
LIM MAMMARY LUMINAL MATURE UP	116	65	All SZGR 2.0 genes in this pathway
WARTERS RESPONSE TO IR SKIN	83	44	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	900	907	1A,m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	900	906	1A	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	900	906	1A	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-142-5p	1165	1172	1A,m8	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-150	1969	1975	1A	hsa-miR-150	UCUCCCAACCCUUGUACCAGUG
miR-18	1057	1063	m8	hsa-miR-18a	UAAGGUGCAUCUAGUGCAGAUA
miR-18	1057	1063	m8	hsa-miR-18b	UAAGGUGCAUCUAGUGCAGUUA
miR-192/215	227	233	m8	hsa-miR-192	CUGACCUAUGAAUUGACAGCC
miR-192/215	227	233	m8	hsa-miR-215	AUGACCUAUGAAUUGACAGAC
miR-223	681	688	1A,m8	hsa-miR-223	UGUCAGUUUGUCAAAUACCCC
miR-299-5p	1758	1764	1A	hsa-miR-299-5p	UGGUUUACCGUCCCACAUACAU
miR-34/449	897	903	m8	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-34b	898	904	m8	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-376c	1133	1140	1A,m8	hsa-miR-376c	AACAUAGAGGAAAUUCCACG
miR-409-3p	1150	1156	1A	hsa-miR-409-3p	CGAAUGUUGCUCGGUGAACCCCU
miR-495	1865	1871	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-495	1865	1871	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-496	304	310	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-496	304	310	1A	hsa-miR-496	AUUACAUGGCCAAUCUC
miR-9	1761	1767	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-9	1761	1767	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: ALCAM