Gene Page:CLGN

Summary?
GeneID 1047
Symbol CLGN
Synonyms -
Description calmegin
Reference MIM:601858|HGNC:HGNC:2060|Ensembl:ENSG00000153132|HPRD:03513|Vega:OTTHUMG00000133414
Gene type protein-coding
Map location 4q28.3-q31.1
Pascal p-value 0.704
Fetal beta 0.674
DMG 1 (# studies)
eGene Cortex
Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
DMG:Jaffe_2016 Genome-wide DNA methylation analysis This 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

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg03575792 4 141348488 CLGN 5.96E-9 -0.008 3.19E-6 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs17050970 chr4 140806020 CLGN 1047 0.02 cis
rs7600825 chr2 20059541 CLGN 1047 0.15 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
死神:胎儿(13 - 26 postconception周),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
NCBP1 0.92 0.93
ZNF134 0.92 0.93
ZMYM4 0.92 0.93
ZNF131 0.92 0.92
HMG20A 0.92 0.94
CSDE1 0.92 0.93
WDR3 0.91 0.92
STRBP 0.91 0.92
WDR48 0.91 0.92
ACTR8 0.91 0.92
Top 10 negatively co-expressed genes
Gene Pearson'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 name Pathway size # SZGR 2.0 genes in pathway Info
GAZDA DIAMOND BLACKFAN ANEMIA PROGENITOR DN 66 42 All SZGR 2.0 genes in this pathway
ZHONG RESPONSE TO AZACITIDINE AND TSA UP 183 119 All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN 663 425 All SZGR 2.0 genes in this pathway
DOANE BREAST CANCER ESR1 UP 112 72 All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP 1278 748 All SZGR 2.0 genes in this pathway
FARMER BREAST CANCER APOCRINE VS BASAL 330 217 All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747 453 All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS DN 193 112 All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM5 94 59 All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK 423 265 All SZGR 2.0 genes in this pathway
OKUMURA INFLAMMATORY RESPONSE LPS 183 115 All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS DN 366 238 All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA MS UP 48 32 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR UP 240 152 All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 3 720 440 All SZGR 2.0 genes in this pathway
LEIN MIDBRAIN MARKERS 82 55 All SZGR 2.0 genes in this pathway
LEIN PONS MARKERS 89 59 All SZGR 2.0 genes in this pathway
LEIN MEDULLA MARKERS 81 48 All SZGR 2.0 genes in this pathway
YEGNASUBRAMANIAN PROSTATE CANCER 128 60 All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN 220 147 All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION DN 105 67 All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN 191 123 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BRAIN DN 85 58 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE UP 97 61 All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN 701 446 All SZGR 2.0 genes in this pathway
MATZUK SPERMATOZOA 114 77 All SZGR 2.0 genes in this pathway
CUI GLUCOSE DEPRIVATION 60 44 All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3 349 234 All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435 318 All SZGR 2.0 genes in this pathway
FONTAINE FOLLICULAR THYROID ADENOMA DN 68 45 All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 2 86 50 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR UP 61 44 All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL 177 132 All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT 572 352 All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A 898 516 All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN 418 245 All SZGR 2.0 genes in this pathway
SMIRNOV RESPONSE TO IR 6HR UP 166 97 All SZGR 2.0 genes in this pathway