Gene Page: COL6A2

Summary ?
GeneID1292
SymbolCOL6A2
SynonymsBTHLM1|PP3610|UCMD1
Descriptioncollagen type VI alpha 2
ReferenceMIM:120240|HGNC:HGNC:2212|Ensembl:ENSG00000142173|HPRD:02110|Vega:OTTHUMG00000090489
Gene typeprotein-coding
Map location21q22.3
Pascal p-value0.019
Sherlock p-value0.005
TADA p-value0.02
Fetal beta0.369
eGeneHippocampus
Myers' cis & trans
SupportCompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
COL6A2chr2147541029GANM_001849
NM_058174
NM_058175		p.484G>R
p.484G>R
p.484G>R		missense
missense
missense		SchizophreniaDNM:Fromer_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17131472chr191962966COL6A212920.02trans
rs3762382chr1198128858COL6A212920.06trans
rs16825495chr2134234401COL6A212920.09trans
rs7651311chr3106820222COL6A212920.18trans
rs2922180chr3125280472COL6A212920.06trans
rs2971271chr3125450402COL6A212920.13trans
rs2976809chr3125451738COL6A212920.01trans
rs313946chr4113975904COL6A212920.19trans
rs17046025chr4166066605COL6A212920.17trans
rs10050805chr530805352COL6A212920.07trans
rs317971chr566688724COL6A212920.06trans
rs12663450chr638135729COL6A212920.14trans
rs4236095chr647368686COL6A212920.1trans
rs6455226chr667930295COL6A212921.834E-4trans
rs7081666chr1047673800COL6A212920.01trans
rs11006556chr1061287609COL6A212920.07trans
rs10879027chr1270237156COL6A212920trans
rs11112163chr12105072508COL6A212920.06trans
rs6095741chr2048666589COL6A212923.888E-8trans
rs5991662chrX43335796COL6A212927.397E-4trans
rs1545676chrX93530472COL6A212920.01trans
rs242163chrX132311662COL6A212920.05trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
GenePearson's Correlation Spearman's Correlation
PLCE10.890.79
IQGAP20.860.66
LTBP10.840.72
EPHB40.840.65
STON10.830.63
FAM111A0.830.79
GLI30.830.73
STON1-GTF2A1L0.830.63
KNTC10.830.58
LIPG0.820.53
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.27-0.35-0.39
AF347015.31-0.34-0.39
C5orf53-0.34-0.34
IFI27-0.34-0.37
MT-CO2-0.34-0.39
HLA-F-0.34-0.26
FBXO2-0.33-0.25
CA4-0.33-0.29
CISD3-0.33-0.35
AF347015.33-0.33-0.34

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG FOCAL ADHESION 201138All SZGR 2.0 genes in this pathway
KEGG ECM RECEPTOR INTERACTION 8453All SZGR 2.0 genes in this pathway
PID INTEGRIN1 PATHWAY 6644All SZGR 2.0 genes in this pathway
PID AVB3 INTEGRIN PATHWAY 7553All SZGR 2.0 genes in this pathway
PID SYNDECAN 1 PATHWAY 4629All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY 396292All SZGR 2.0 genes in this pathway
REACTOME EXTRACELLULAR MATRIX ORGANIZATION 8742All SZGR 2.0 genes in this pathway
REACTOME COLLAGEN FORMATION 5831All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY PDGF 12293All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE 251188All SZGR 2.0 genes in this pathway
REACTOME NCAM1 INTERACTIONS 3927All SZGR 2.0 genes in this pathway
REACTOME NCAM SIGNALING FOR NEURITE OUT GROWTH 6449All SZGR 2.0 genes in this pathway
SCHUETZ BREAST CANCER DUCTAL INVASIVE UP 351230All SZGR 2.0 genes in this pathway
DAVICIONI TARGETS OF PAX FOXO1 FUSIONS UP 255177All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA UP 368234All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL DN 460312All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER BASAL VS MESENCHYMAL DN 5036All SZGR 2.0 genes in this pathway
GAL LEUKEMIC STEM CELL DN 244153All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS F UP 185119All SZGR 2.0 genes in this pathway
BERENJENO TRANSFORMED BY RHOA DN 394258All SZGR 2.0 genes in this pathway
HUMMERICH SKIN CANCER PROGRESSION DN 10064All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2B 392251All SZGR 2.0 genes in this pathway
MURATA VIRULENCE OF H PILORI 2416All SZGR 2.0 genes in this pathway
WU CELL MIGRATION 184114All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 21Q22 AMPLICON 1611All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 UP 256159All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS SUBSET 3320All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP 266171All SZGR 2.0 genes in this pathway
JECHLINGER EPITHELIAL TO MESENCHYMAL TRANSITION UP 7151All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA PROGNOSIS UP 4730All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT UP 8961All SZGR 2.0 genes in this pathway
IGLESIAS E2F TARGETS UP 151103All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA DN 408274All SZGR 2.0 genes in this pathway
JIANG AGING CEREBRAL CORTEX UP 3627All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS UP 3727All SZGR 2.0 genes in this pathway
HEDENFALK BREAST CANCER BRACX UP 2014All SZGR 2.0 genes in this pathway
PAL PRMT5 TARGETS UP 203135All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 16911088All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN 504323All SZGR 2.0 genes in this pathway
ZHU CMV 24 HR DN 9164All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 18HR DN 178121All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 4 4832All SZGR 2.0 genes in this pathway
ZHU CMV ALL DN 12893All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 UP 428266All SZGR 2.0 genes in this pathway
JACKSON DNMT1 TARGETS DN 2521All SZGR 2.0 genes in this pathway
HAN JNK SINGALING DN 3927All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP 566371All SZGR 2.0 genes in this pathway
CLASPER LYMPHATIC VESSELS DURING METASTASIS DN 3623All SZGR 2.0 genes in this pathway
HARRIS BRAIN CANCER PROGENITORS 4423All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP 461298All SZGR 2.0 genes in this pathway
LEE METASTASIS AND ALTERNATIVE SPLICING UP 7451All SZGR 2.0 genes in this pathway
MARTINEZ RB1 TARGETS UP 673430All SZGR 2.0 genes in this pathway
MARTINEZ TP53 TARGETS DN 593372All SZGR 2.0 genes in this pathway
MARTINEZ RB1 AND TP53 TARGETS DN 591366All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN 191123All SZGR 2.0 genes in this pathway
MISHRA CARCINOMA ASSOCIATED FIBROBLAST UP 2414All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY DN 5839All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL UP 260174All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA DN 10063All SZGR 2.0 genes in this pathway
TSAI RESPONSE TO RADIATION THERAPY 3220All SZGR 2.0 genes in this pathway
GU PDEF TARGETS UP 7149All SZGR 2.0 genes in this pathway
SCHRAETS MLL TARGETS DN 3324All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN 435289All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP 395249All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS DN 442275All SZGR 2.0 genes in this pathway
MIKKELSEN DEDIFFERENTIATED STATE DN 77All SZGR 2.0 genes in this pathway
MEISSNER ES ICP WITH H3K4ME3 3417All SZGR 2.0 genes in this pathway
MEISSNER NPC ICP WITH H3 UNMETHYLATED 2415All SZGR 2.0 genes in this pathway
MEISSNER BRAIN ICP WITH H3K4ME3 3217All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED 351238All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S1 237159All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 16 7947All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 30MIN UP 5638All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572352All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567365All SZGR 2.0 genes in this pathway
QI HYPOXIA TARGETS OF HIF1A AND FOXA2 3727All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP 504321All SZGR 2.0 genes in this pathway
LEE BMP2 TARGETS UP 745475All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN 1080713All SZGR 2.0 genes in this pathway
KATSANOU ELAVL1 TARGETS DN 14888All SZGR 2.0 genes in this pathway
WANG MLL TARGETS 289188All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE NOT VIA P38 337236All SZGR 2.0 genes in this pathway
ANASTASSIOU CANCER MESENCHYMAL TRANSITION SIGNATURE 6440All SZGR 2.0 genes in this pathway
LIM MAMMARY LUMINAL MATURE DN 9974All SZGR 2.0 genes in this pathway
DURAND STROMA S UP 297194All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All SZGR 2.0 genes in this pathway
NABA COLLAGENS 4426All SZGR 2.0 genes in this pathway
NABA CORE MATRISOME 275148All SZGR 2.0 genes in this pathway
NABA BASEMENT MEMBRANES 4022All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028559All SZGR 2.0 genes in this pathway