Gene Page: CHI3L1

Summary ?
GeneID1116
SymbolCHI3L1
SynonymsASRT7|CGP-39|GP-39|GP39|HC-gp39|HCGP-3P|YKL-40|YKL40|YYL-40|hCGP-39
Descriptionchitinase 3 like 1
ReferenceMIM:601525|HGNC:HGNC:1932|Ensembl:ENSG00000133048|HPRD:03314|Vega:OTTHUMG00000042122
Gene typeprotein-coding
Map location1q32.1
Sherlock p-value0.005
Fetal beta-2.049
DMG1 (# studies)
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
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
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 studies2Link to SZGene
ExpressionMeta-analysis of gene expressionP value: 1.507 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg036259111203155737CHI3L11.686E-40.4160.033DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17541094chr266266798CHI3L111160.03trans
rs10497429chr2175600890CHI3L111160.04trans
rs10513763chr3179386743CHI3L111160.01trans
rs17237063chr3182134513CHI3L111160.17trans
rs10515260chr597076547CHI3L111160.12trans
rs11833888chr1259350152CHI3L111160.13trans

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
NKAIN20.860.89
LGALS80.860.87
RP11-791G16.20.850.88
RBM240.850.90
DOCK90.850.85
PPFIA20.840.88
RNF19A0.840.84
SLITRK50.830.87
AC079061.10.820.89
RHOBTB10.820.86
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
FXYD1-0.65-0.66
HSD17B14-0.64-0.67
MT-CO2-0.64-0.67
AF347015.31-0.63-0.66
TSC22D4-0.62-0.63
SLC25A18-0.62-0.63
TLCD1-0.62-0.66
AF347015.33-0.62-0.63
ACSF2-0.62-0.68
AIFM3-0.62-0.59

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0003824catalytic activityIEA-
GO:0005529sugar bindingIEA-
GO:0004568chitinase activityIEA-
GO:0004553hydrolase activity, hydrolyzing O-glycosyl compoundsIEA-
GO:0005201extracellular matrix structural constituentTAS8245017 
GO:0005215transporter activityIEA-
GO:0043169cation bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006032chitin catabolic processIEA-
GO:0005975carbohydrate metabolic processIEA-
GO:0006810transportIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-
GO:0005578proteinaceous extracellular matrixTAS8245017 
GO:0005615extracellular spaceTAS8245017 
GO:0016020membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN 634384All SZGR 2.0 genes in this pathway
PICCALUGA ANGIOIMMUNOBLASTIC LYMPHOMA UP 205140All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA UP 294178All SZGR 2.0 genes in this pathway
TURASHVILI BREAST DUCTAL CARCINOMA VS DUCTAL NORMAL DN 198110All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485293All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY UP 430232All SZGR 2.0 genes in this pathway
SMIRNOV CIRCULATING ENDOTHELIOCYTES IN CANCER UP 158103All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 8D DN 205127All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 10D DN 14290All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 16D DN 14383All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 DN 242165All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN 281186All SZGR 2.0 genes in this pathway
LOPEZ MESOTHELIOMA SURVIVAL WORST VS BEST DN 76All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP 557331All SZGR 2.0 genes in this pathway
SABATES COLORECTAL ADENOMA UP 14175All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL DN 226132All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375806All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP 443294All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 UP 12073All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 3 4WK UP 214144All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 4 5WK UP 271175All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 6 7WK UP 197135All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS DN 6244All SZGR 2.0 genes in this pathway
DARWICHE SKIN TUMOR PROMOTER UP 14296All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK LOW UP 162104All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK HIGH UP 147101All SZGR 2.0 genes in this pathway
DARWICHE SQUAMOUS CELL CARCINOMA UP 146104All SZGR 2.0 genes in this pathway
CAVARD LIVER CANCER MALIGNANT VS BENIGN 3219All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER BASAL VS LULMINAL 330215All SZGR 2.0 genes in this pathway
YANG BREAST CANCER ESR1 LASER DN 5038All SZGR 2.0 genes in this pathway
COLIN PILOCYTIC ASTROCYTOMA VS GLIOBLASTOMA DN 2821All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN 357212All SZGR 2.0 genes in this pathway
ROSS AML WITH CBFB MYH11 FUSION 5232All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA DESMOPLASIC VS CLASSIC UP 6238All SZGR 2.0 genes in this pathway
LENAOUR DENDRITIC CELL MATURATION DN 12890All SZGR 2.0 genes in this pathway
VERHAAK AML WITH NPM1 MUTATED DN 246180All SZGR 2.0 genes in this pathway
MARIADASON REGULATED BY HISTONE ACETYLATION UP 8349All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES DN 245144All SZGR 2.0 genes in this pathway
LIANG SILENCED BY METHYLATION UP 3218All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN 434302All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 419273All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP 280183All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES UP 253147All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP 953554All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN 911527All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP 783442All SZGR 2.0 genes in this pathway
DURCHDEWALD SKIN CARCINOGENESIS DN 264168All SZGR 2.0 genes in this pathway
STEARMAN TUMOR FIELD EFFECT UP 3622All SZGR 2.0 genes in this pathway
STEARMAN LUNG CANCER EARLY VS LATE UP 12589All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION UP 282183All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN 191123All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B DN 564326All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476285All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP 648398All SZGR 2.0 genes in this pathway
WILENSKY RESPONSE TO DARAPLADIB 2920All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP 425298All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 UP 338225All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP 418282All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 UP 408276All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER ESR1 DN 240153All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP 491316All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 9 3526All SZGR 2.0 genes in this pathway
POOLA INVASIVE BREAST CANCER DN 13483All SZGR 2.0 genes in this pathway
KYNG WERNER SYNDROM AND NORMAL AGING DN 225124All SZGR 2.0 genes in this pathway
NOUSHMEHR GBM SILENCED BY METHYLATION 5032All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP 857456All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA MESENCHYMAL 216130All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572352All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 19721213All SZGR 2.0 genes in this pathway
MIYAGAWA TARGETS OF EWSR1 ETS FUSIONS DN 229135All 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
HECKER IFNB1 TARGETS 9554All SZGR 2.0 genes in this pathway