Gene Page: CHGA

Summary ?
GeneID1113
SymbolCHGA
SynonymsCGA
Descriptionchromogranin A
ReferenceMIM:118910|HGNC:HGNC:1929|Ensembl:ENSG00000100604|HPRD:07170|Vega:OTTHUMG00000171225
Gene typeprotein-coding
Map location14q32
Pascal p-value0.203
Sherlock p-value0.966
Fetal beta-1.516
eGeneCerebellum
Myers' cis & trans
SupportNEUROTROPHIN SIGNALING

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
AssociationA combined odds ratio method (Sun et al. 2008), association studies3Link to SZGene
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6048101chr2022429986CHGA11130.13trans
rs6036116chr2022430349CHGA11130.16trans
rs4632416chr2022437090CHGA11130.11trans
rs4459793chr2022439811CHGA11130.15trans
rs6048112chr2022442814CHGA11130.08trans

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
MAP2K40.940.92
FAM179B0.940.91
FAM126B0.940.91
NCOA70.940.91
CLOCK0.930.91
COL4A3BP0.930.92
DPP80.930.89
ADAM220.920.90
SYT10.920.88
HOOK10.920.87
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
EFEMP2-0.48-0.50
RAB34-0.45-0.52
EIF4EBP3-0.43-0.49
C1orf61-0.43-0.58
GATSL3-0.42-0.44
DBI-0.42-0.49
NUDT8-0.41-0.45
RAB13-0.39-0.48
BCL7C-0.38-0.39
NKAIN4-0.38-0.47

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005509calcium ion bindingIEA-
GO:0005515protein bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0008217regulation of blood pressureTAS8406464 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
BASAKI YBX1 TARGETS DN 384230All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY DN 367220All SZGR 2.0 genes in this pathway
LEE NEURAL CREST STEM CELL UP 14699All SZGR 2.0 genes in this pathway
SABATES COLORECTAL ADENOMA DN 291176All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN DN 172112All SZGR 2.0 genes in this pathway
BARRIER CANCER RELAPSE NORMAL SAMPLE UP 3221All SZGR 2.0 genes in this pathway
WANG BARRETTS ESOPHAGUS UP 5127All SZGR 2.0 genes in this pathway
RORIE TARGETS OF EWSR1 FLI1 FUSION DN 3023All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
WANG LSD1 TARGETS DN 3930All SZGR 2.0 genes in this pathway
AMUNDSON GAMMA RADIATION RESISTANCE 2014All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B UP 172109All SZGR 2.0 genes in this pathway
BOCHKIS FOXA2 TARGETS 425261All SZGR 2.0 genes in this pathway
VART KSHV INFECTION ANGIOGENIC MARKERS DN 13892All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS DN 366257All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3 590403All SZGR 2.0 genes in this pathway
HOFFMAN CLOCK TARGETS DN 106All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP 548370All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A 898516All SZGR 2.0 genes in this pathway
ROLEF GLIS3 TARGETS 3729All SZGR 2.0 genes in this pathway