Gene Page: COL2A1

Summary ?
GeneID1280
SymbolCOL2A1
SynonymsANFH|AOM|COL11A3|SEDC|STL1
Descriptioncollagen type II alpha 1
ReferenceMIM:120140|HGNC:HGNC:2200|Ensembl:ENSG00000139219|HPRD:00361|Vega:OTTHUMG00000149896
Gene typeprotein-coding
Map location12q13.11
Pascal p-value0.032
Fetal beta1
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWAScatGenome-wide Association StudiesThis data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg117218031248398380COL2A12.018E-4-0.2230.035DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs10994209chr1061877705COL2A112800.13trans

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
NID10.830.73
COL11A10.780.73
COL1A20.770.75
NID20.760.73
CPAMD80.760.50
ADAMTS120.760.60
COL1A10.760.62
HSPG20.760.70
SVIL0.760.67
EPHB40.750.63
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C5orf53-0.37-0.43
AF347015.31-0.36-0.48
AF347015.27-0.36-0.47
AF347015.33-0.36-0.46
MT-CO2-0.35-0.49
S100B-0.35-0.46
MT-CYB-0.34-0.44
FXYD1-0.34-0.43
AF347015.8-0.34-0.46
HLA-F-0.34-0.31

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
ANXA5ANX5 | ENX2 | PP4annexin A5-HPRD,BioGRID1397263 
BGNDSPG1 | PG-S1 | PGI | SLRR1Abiglycan-HPRD,BioGRID2059554 
BMP2BMP2Abone morphogenetic protein 2-HPRD,BioGRID10085302 
C1QA-complement component 1, q subcomponent, A chain-HPRD,BioGRID8778019 
CHADSLRR4Achondroadherin-HPRD11445564 
COL2A1ANFH | AOM | COL11A3 | MGC131516 | SEDCcollagen, type II, alpha 1-HPRD,BioGRID1556676 |8660302 
|11724554 
COL6A1OPLLcollagen, type VI, alpha 1-HPRD1544908 
COL9A1DJ149L1.1.2 | EDM6 | FLJ40263 | MEDcollagen, type IX, alpha 1Reconstituted ComplexBioGRID11724554 
COL9A2DJ39G22.4 | EDM2 | MEDcollagen, type IX, alpha 2-HPRD11724554 
COL9A3DJ885L7.4.1 | EDM3 | FLJ90759 | IDD | MEDcollagen, type IX, alpha 3-HPRD11724554 
COMPEDM1 | EPD1 | MED | MGC131819 | MGC149768 | PSACH | THBS5cartilage oligomeric matrix protein-HPRD,BioGRID9685393 
DCNCSCD | DSPG2 | PG40 | PGII | PGS2 | SLRR1Bdecorin-HPRD10382266 
DDR1CAK | CD167 | DDR | EDDR1 | MCK10 | NEP | NTRK4 | PTK3 | PTK3A | RTK6 | TRKEdiscoidin domain receptor tyrosine kinase 1-HPRD9659900 
FGF7HBGF-7 | KGFfibroblast growth factor 7 (keratinocyte growth factor)-HPRD,BioGRID11973338 
FN1CIG | DKFZp686F10164 | DKFZp686H0342 | DKFZp686I1370 | DKFZp686O13149 | ED-B | FINC | FN | FNZ | GFND | GFND2 | LETS | MSFfibronectin 1-HPRD,BioGRID2229073 |3997552 
ITGA2BCD41 | CD41B | GP2B | GPIIb | GTA | HPA3integrin, alpha 2b (platelet glycoprotein IIb of IIb/IIIa complex, antigen CD41)-HPRD,BioGRID7520045 |10772239 
LOXL4FLJ21889 | LOXClysyl oxidase-like 4-HPRD11292829 
MAGGMA | S-MAG | SIGLEC-4A | SIGLEC4Amyelin associated glycoprotein-HPRD,BioGRID2446864 
MATN1CMP | CRTMmatrilin 1, cartilage matrix protein-HPRD10196235 
PKD1PBPpolycystic kidney disease 1 (autosomal dominant)-HPRD,BioGRID11406351 
PRELPMGC45323 | MST161 | MSTP161 | SLRR2Aproline/arginine-rich end leucine-rich repeat protein-HPRD,BioGRID11847210 
SPARCONsecreted protein, acidic, cysteine-rich (osteonectin)-HPRD2745554 
TGFB1CED | DPD1 | TGFB | TGFbetatransforming growth factor, beta 1-HPRD,BioGRID10085302 
TGFBIBIGH3 | CDB1 | CDG2 | CDGG1 | CSD | CSD1 | CSD2 | CSD3 | EBMD | LCD1transforming growth factor, beta-induced, 68kDa-HPRD9061001 
THBS1THBS | TSP | TSP1thrombospondin 1-HPRD,BioGRID3571333 
TNFRSF10AAPO2 | CD261 | DR4 | MGC9365 | TRAILR-1 | TRAILR1tumor necrosis factor receptor superfamily, member 10a-HPRD,BioGRID9811967 


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 INTEGRIN CELL SURFACE INTERACTIONS 7948All 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
GAZDA DIAMOND BLACKFAN ANEMIA ERYTHROID DN 493298All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL UP 233161All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP 456228All SZGR 2.0 genes in this pathway
ODONNELL METASTASIS UP 8258All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS A DN 9061All SZGR 2.0 genes in this pathway
PEREZ TP53 TARGETS 1174695All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP 390236All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN 848527All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038678All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062725All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS 652441All SZGR 2.0 genes in this pathway
ROSS AML WITH PML RARA FUSION 7762All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA DESMOPLASIC VS CLASSIC UP 6238All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 1 DN 163115All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP 240152All SZGR 2.0 genes in this pathway
KAYO CALORIE RESTRICTION MUSCLE DN 8759All SZGR 2.0 genes in this pathway
KAAB HEART ATRIUM VS VENTRICLE UP 249170All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN 287208All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 6HR UP 7148All SZGR 2.0 genes in this pathway
KRASNOSELSKAYA ILF3 TARGETS DN 4638All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 3 720440All SZGR 2.0 genes in this pathway
RIZKI TUMOR INVASIVENESS 3D DN 270181All SZGR 2.0 genes in this pathway
FUJII YBX1 TARGETS DN 202132All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE DN 315197All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN LUNG UP 2110All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP 648398All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS 425261All SZGR 2.0 genes in this pathway
HELLEBREKERS SILENCED DURING TUMOR ANGIOGENESIS 8056All SZGR 2.0 genes in this pathway
LI WILMS TUMOR 2712All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER POOR SURVIVAL A6 456285All SZGR 2.0 genes in this pathway
COLINA TARGETS OF 4EBP1 AND 4EBP2 356214All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME2 AND H3K27ME3 5935All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway
NAKAYAMA FGF2 TARGETS 2917All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S2 11574All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA1 DN 7447All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA2 UP 8750All SZGR 2.0 genes in this pathway
NIELSEN SYNOVIAL SARCOMA UP 1814All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 30MIN UP 5638All SZGR 2.0 genes in this pathway
WANG METASTASIS OF BREAST CANCER 158All SZGR 2.0 genes in this pathway
KANG AR TARGETS UP 1710All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP 504321All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 NOT SATB1 UP 344215All SZGR 2.0 genes in this pathway
PLASARI NFIC TARGETS BASAL UP 2717All SZGR 2.0 genes in this pathway
PLASARI TGFB1 SIGNALING VIA NFIC 1HR DN 10677All SZGR 2.0 genes in this pathway
PLASARI TGFB1 SIGNALING VIA NFIC 10HR UP 5438All SZGR 2.0 genes in this pathway
WANG MLL TARGETS 289188All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS UP 266142All 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 MATRISOME 1028559All SZGR 2.0 genes in this pathway