Gene Page:LRRC1

Summary?
GeneID 55227
Symbol LRRC1
Synonyms LANO|dJ523E19.1
Description leucine rich repeat containing 1
Reference MIM:608195|HGNC:HGNC:14307|Ensembl:ENSG00000137269|Vega:OTTHUMG00000014885
Gene type protein-coding
Map location 6p12.1
Pascal p-value 0.115
Sherlock p-value 0.112
DEG p-value DEG:Zhao_2015:p=6.97e-04:q=0.0984
Fetal beta 1.348
DMG 1 (# studies)
eGene Myers' cis & trans

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
DEG:Zhao_2015 RNA Sequencing analysis Transcriptome sequencing and genome-wide association analyses reveal lysosomal function and actin cytoskeleton remodeling in schizophrenia and bipolar disorder.
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
GSMA_IIE Genome scan meta-analysis (European-ancestry samples) Psr: 0.04433

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg15286372 6 53659348 LRRC1 4.47E-8 -0.015 1.22E-5 DMG:Jaffe_2016

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs1346726 chr8 27335218 LRRC1 55227 0.2 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
RBM14 0.93 0.90
CCDC71 0.93 0.94
PCIF1 0.93 0.92
ZNF574 0.92 0.89
USP21 0.92 0.91
TOR2A 0.92 0.91
SMPD4 0.91 0.89
DCAKD 0.91 0.89
FAM127C 0.91 0.88
RSAD1 0.91 0.89
Top 10 negatively co-expressed genes
Gene Pearson's Correlation Spearman's Correlation
AF347015.27 -0.69 -0.82
AF347015.31 -0.69 -0.81
MT-CO2 -0.67 -0.80
AF347015.8 -0.66 -0.81
MT-CYB -0.66 -0.80
AF347015.33 -0.65 -0.77
C5orf53 -0.64 -0.69
AF347015.15 -0.63 -0.79
AF347015.21 -0.63 -0.85
AF347015.2 -0.60 -0.77

Section III. Gene Ontology annotation

Molecular function 去的术语 Evidence Neuro keywords PubMed ID
GO:0005515 protein binding IEA -
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0005737 cytoplasm IEA -
GO:0016020 membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
ONKEN UVEAL MELANOMA DN 526 357 All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS UP 306 188 All SZGR 2.0 genes in this pathway
OSWALD HEMATOPOIETIC STEM CELL IN COLLAGEN GEL DN 275 168 All SZGR 2.0 genes in this pathway
SENESE HDAC1 AND HDAC2 TARGETS DN 232 139 All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA DN 284 156 All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 DN 464 276 All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP 1691 1088 All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR 681 420 All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE UP 578 341 All SZGR 2.0 genes in this pathway
CHIANG LIVER CANCER SUBCLASS PROLIFERATION UP 178 108 All SZGR 2.0 genes in this pathway
LOPEZ EPITHELIOID MESOTHELIOMA 17 11 All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA UP 207 143 All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES UP 605 377 All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 24HR DN 505 328 All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 1ST EGF PULSE ONLY 1839 928 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
miR-124.1 595 601 m8 hsa-miR-124a UUAAGGCACGCGGUGAAUGCCA
miR-124/506 594 601 1A,m8 hsa-miR-506 UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brain UAAGGCACGCGGUGAAUGCC
miR-134 1255 1261 m8 hsa-miR-134brain UGUGACUGGUUGACCAGAGGG
miR-142-3p 245 251 m8 hsa-miR-142-3p UGUAGUGUUUCCUACUUUAUGGA
miR-22 434 440 m8 hsa-miR-22brain AAGCUGCCAGUUGAAGAACUGU
miR-381 464 470 1A hsa-miR-381 UAUACAAGGGCAAGCUCUCUGU
miR-495 502 508 1A hsa-miR-495brain AAACAAACAUGGUGCACUUCUUU
miR-544 919 925 1A hsa-miR-544 AUUCUGCAUUUUUAGCAAGU
miR-9 794 800 m8 hsa-miR-9SZ UCUUUGGUUAUCUAGCUGUAUGA