Gene Page: CLGN

Summary ?
GeneID1047
SymbolCLGN
Synonyms-
Descriptioncalmegin
ReferenceMIM:601858|HGNC:HGNC:2060|Ensembl:ENSG00000153132|HPRD:03513|Vega:OTTHUMG00000133414
Gene typeprotein-coding
Map location4q28.3-q31.1
Pascal p-value0.704
Fetal beta0.674
DMG1 (# studies)
eGeneCortex
Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg035757924141348488CLGN5.96E-9-0.0083.19E-6DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs17050970chr4140806020CLGN10470.02cis
rs7600825chr220059541CLGN10470.15trans

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
NCBP10.920.93
ZNF1340.920.93
ZMYM40.920.93
ZNF1310.920.92
HMG20A0.920.94
CSDE10.920.93
WDR30.910.92
STRBP0.910.92
WDR480.910.92
ACTR80.910.92
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
FXYD1-0.75-0.86
MT-CO2-0.73-0.82
AF347015.31-0.72-0.82
AF347015.27-0.72-0.82
AF347015.33-0.72-0.80
IFI27-0.71-0.84
AF347015.8-0.71-0.82
AC021016.1-0.70-0.80
TSC22D4-0.70-0.78
MT-CYB-0.69-0.79

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
GAZDA DIAMOND BLACKFAN ANEMIA PROGENITOR DN 6642All SZGR 2.0 genes in this pathway
ZHONG RESPONSE TO AZACITIDINE AND TSA UP 183119All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN 663425All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER ESR1 UP 11272All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP 1278748All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS BASAL 330217All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS DN 193112All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM5 9459All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK 423265All SZGR 2.0 genes in this pathway
OKUMURA INFLAMMATORY RESPONSE LPS 183115All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS DN 366238All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA MS UP 4832All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP 240152All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 3 720440All SZGR 2.0 genes in this pathway
LEIN MIDBRAIN MARKERS 8255All SZGR 2.0 genes in this pathway
LEIN PONS MARKERS 8959All SZGR 2.0 genes in this pathway
LEIN MEDULLA MARKERS 8148All SZGR 2.0 genes in this pathway
YEGNASUBRAMANIAN PROSTATE CANCER 12860All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN 220147All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION DN 10567All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN 191123All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BRAIN DN 8558All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE UP 9761All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN 701446All SZGR 2.0 genes in this pathway
MATZUK SPERMATOZOA 11477All SZGR 2.0 genes in this pathway
CUI GLUCOSE DEPRIVATION 6044All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3 349234All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435318All SZGR 2.0 genes in this pathway
FONTAINE FOLLICULAR THYROID ADENOMA DN 6845All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 2 8650All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR UP 6144All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL 177132All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572352All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A 898516All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN 418245All SZGR 2.0 genes in this pathway
SMIRNOV RESPONSE TO IR 6HR UP 16697All SZGR 2.0 genes in this pathway