Gene Page:CHI3L1

Summary?
GeneID 1116
Symbol CHI3L1
Synonyms ASRT7|CGP-39|GP-39|GP39|HC-gp39|HCGP-3P|YKL-40|YKL40|YYL-40|hCGP-39
Description chitinase 3 like 1
Reference MIM:601525|HGNC:HGNC:1932|Ensembl:ENSG00000133048|HPRD:03314|Vega:OTTHUMG00000042122
Gene type protein-coding
Map location 1q32.1
Sherlock p-value 0.005
Fetal beta -2.049
DMG 1 (# studies)
eGene Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:GWASdb Genome-wide Association Studies GWASdb records for schizophrenia
CV:PGCnp Genome-wide Association Study GWAS
DMG:Wockner_2014 Genome-wide DNA methylation analysis This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association A combined odds ratio method (Sun et al. 2008), association studies 2 Link to SZGene
Expression Meta-analysis of gene expression Pvalue: 1.507
Literature High-throughput literature-search Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenias Click to show details

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg03625911 1 203155737 CHI3L1 1.686E-4 0.416 0.033 DMG:Wockner_2014

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs17541094 chr2 66266798 CHI3L1 1116 0.03 trans
rs10497429 chr2 175600890 CHI3L1 1116 0.04 trans
rs10513763 chr3 179386743 CHI3L1 1116 0.01 trans
rs17237063 chr3 182134513 CHI3L1 1116 0.17 trans
rs10515260 chr5 97076547 CHI3L1 1116 0.12 trans
rs11833888 chr12 59350152 CHI3L1 1116 0.13 trans

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
Gene Pearson's Correlation Spearman's Correlation
NKAIN2 0.86 0.89
LGALS8 0.86 0.87
RP11-791G16.2 0.85 0.88
RBM24 0.85 0.90
DOCK9 0.85 0.85
PPFIA2 0.84 0.88
RNF19A 0.84 0.84
SLITRK5 0.83 0.87
AC079061.1 0.82 0.89
RHOBTB1 0.82 0.86
Top 10 negatively co-expressed genes
Gene Pearson'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 function GO term Evidence Neuro keywords PubMed ID
GO:0003824 catalytic activity IEA -
GO:0005529 sugar binding IEA -
GO:0004568 chitinase activity IEA -
GO:0004553 hydrolase activity, hydrolyzing O-glycosyl compounds IEA -
GO:0005201 extracellular matrix structural constituent TAS 8245017
GO:0005215 transporter activity IEA -
GO:0043169 cation binding IEA -
Biological process GO term Evidence Neuro keywords PubMed ID
GO:0006032 chitin catabolic process IEA -
GO:0005975 carbohydrate metabolic process IEA -
GO:0006810 transport IEA -
Cellular component GO term Evidence Neuro keywords PubMed ID
GO:0005576 extracellular region IEA -
GO:0005578 proteinaceous extracellular matrix TAS 8245017
GO:0005615 extracellular space TAS 8245017
GO:0016020 membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN 634 384 All SZGR 2.0 genes in this pathway
PICCALUGA ANGIOIMMUNOBLASTIC LYMPHOMA UP 205 140 All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA UP 294 178 All SZGR 2.0 genes in this pathway
TURASHVILI BREAST DUCTAL CARCINOMA VS DUCTAL NORMAL DN 198 110 All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP 485 293 All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY UP 430 232 All SZGR 2.0 genes in this pathway
SMIRNOV CIRCULATING ENDOTHELIOCYTES IN CANCER UP 158 103 All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 8D DN 205 127 All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 10D DN 142 90 All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 16D DN 143 83 All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 DN 242 165 All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 DN 281 186 All SZGR 2.0 genes in this pathway
LOPEZ MESOTHELIOMA SURVIVAL WORST VS BEST DN 7 6 All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP 557 331 All SZGR 2.0 genes in this pathway
SABATES COLORECTAL ADENOMA UP 141 75 All SZGR 2.0 genes in this pathway
JAATINEN HEMATOPOIETIC STEM CELL DN 226 132 All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN 1375 806 All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP 443 294 All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 UP 120 73 All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 3 4WK UP 214 144 All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 4 5WK UP 271 175 All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL BREAST 6 7WK UP 197 135 All SZGR 2.0 genes in this pathway
MCBRYAN PUBERTAL TGFB1 TARGETS DN 62 44 All SZGR 2.0 genes in this pathway
DARWICHE SKIN TUMOR PROMOTER UP 142 96 All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK LOW UP 162 104 All SZGR 2.0 genes in this pathway
DARWICHE PAPILLOMA RISK HIGH UP 147 101 All SZGR 2.0 genes in this pathway
DARWICHE SQUAMOUS CELL CARCINOMA UP 146 104 All SZGR 2.0 genes in this pathway
CAVARD LIVER CANCER MALIGNANT VS BENIGN 32 19 All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER BASAL VS LULMINAL 330 215 All SZGR 2.0 genes in this pathway
YANG BREAST CANCER ESR1 LASER DN 50 38 All SZGR 2.0 genes in this pathway
COLIN PILOCYTIC ASTROCYTOMA VS GLIOBLASTOMA DN 28 21 All SZGR 2.0 genes in this pathway
沈SMARCA2 DN的目标 357 212 All SZGR 2.0 genes in this pathway
ROSS AML WITH CBFB MYH11 FUSION 52 32 All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA DESMOPLASIC VS CLASSIC UP 62 38 All SZGR 2.0 genes in this pathway
LENAOUR DENDRITIC CELL MATURATION DN 128 90 All SZGR 2.0 genes in this pathway
VERHAAK AML WITH NPM1 MUTATED DN 246 180 All SZGR 2.0 genes in this pathway
MARIADASON REGULATED BY HISTONE ACETYLATION UP 83 49 All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES DN 245 144 All SZGR 2.0 genes in this pathway
LIANG SILENCED BY METHYLATION UP 32 18 All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN 434 302 All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 419 273 All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS UP 280 183 All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES UP 253 147 All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP 953 554 All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN 911 527 All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP 783 442 All SZGR 2.0 genes in this pathway
DURCHDEWALD SKIN CARCINOGENESIS DN 264 168 All SZGR 2.0 genes in this pathway
STEARMAN TUMOR FIELD EFFECT UP 36 22 All SZGR 2.0 genes in this pathway
STEARMAN LUNG CANCER EARLY VS LATE UP 125 89 All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION UP 282 183 All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN 191 123 All SZGR 2.0 genes in this pathway
乳腺癌萧述三腔的DN 564 326 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476 285 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP 648 398 All SZGR 2.0 genes in this pathway
WILENSKY RESPONSE TO DARAPLADIB 29 20 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
RUTELLA RESPONSE TO CSF2RB AND IL4 UP 338 225 All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP 418 282 All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 UP 408 276 All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER ESR1 DN 240 153 All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS UP 491 316 All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 9 35 26 All SZGR 2.0 genes in this pathway
POOLA INVASIVE BREAST CANCER DN 134 83 All SZGR 2.0 genes in this pathway
KYNG WERNER SYNDROM AND NORMAL AGING DN 225 124 All SZGR 2.0 genes in this pathway
NOUSHMEHR GBM SILENCED BY METHYLATION 50 32 All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP 857 456 All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA MESENCHYMAL 216 130 All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572 352 All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS DN 1972 1213 All SZGR 2.0 genes in this pathway
MIYAGAWA TARGETS OF EWSR1 ETS FUSIONS DN 229 135 All SZGR 2.0 genes in this pathway
WANG MLL TARGETS 289 188 All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS UP 266 142 All SZGR 2.0 genes in this pathway
HECKER IFNB1 TARGETS 95 54 All SZGR 2.0 genes in this pathway