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Gene: LRRC1 |
Gene summary for LRRC1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LRRC1 | Gene ID | 55227 |
Gene name | leucine rich repeat containing 1 | |
Gene Alias | LANO | |
Cytomap | 6p12.1 | |
Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | Q9BTT6 |
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Malignant transformation analysis |
Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
Malignant transformation involving gene list. |
Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
55227 | LRRC1 | P75T-E | Human | Esophagus | ESCC | 3.53e-26 | 4.71e-01 | 0.1125 |
55227 | LRRC1 | P76T-E | Human | Esophagus | ESCC | 7.80e-20 | 2.47e-01 | 0.1207 |
55227 | LRRC1 | P79T-E | Human | Esophagus | ESCC | 9.69e-19 | 3.40e-01 | 0.1154 |
55227 | LRRC1 | P80T-E | Human | Esophagus | ESCC | 1.85e-28 | 8.33e-01 | 0.155 |
55227 | LRRC1 | P82T-E | Human | Esophagus | ESCC | 4.82e-16 | 5.63e-01 | 0.1072 |
55227 | LRRC1 | P83T-E | Human | Esophagus | ESCC | 1.91e-07 | 2.08e-01 | 0.1738 |
55227 | LRRC1 | P84T-E | Human | Esophagus | ESCC | 3.59e-03 | 2.89e-01 | 0.0933 |
55227 | LRRC1 | P89T-E | Human | Esophagus | ESCC | 3.62e-06 | 3.71e-01 | 0.1752 |
55227 | LRRC1 | P104T-E | Human | Esophagus | ESCC | 6.34e-04 | 2.01e-01 | 0.0931 |
55227 | LRRC1 | P107T-E | Human | Esophagus | ESCC | 4.15e-08 | 2.57e-01 | 0.171 |
55227 | LRRC1 | P126T-E | Human | Esophagus | ESCC | 3.58e-04 | 4.36e-01 | 0.1125 |
55227 | LRRC1 | P127T-E | Human | Esophagus | ESCC | 3.03e-10 | 2.45e-01 | 0.0826 |
55227 | LRRC1 | P128T-E | Human | Esophagus | ESCC | 2.00e-15 | 4.89e-01 | 0.1241 |
55227 | LRRC1 | P130T-E | Human | Esophagus | ESCC | 1.22e-40 | 7.82e-01 | 0.1676 |
55227 | LRRC1 | RNA-P17T-P17T-4 | Human | Lung | IAC | 8.15e-05 | 5.69e-01 | 0.343 |
55227 | LRRC1 | RNA-P17T-P17T-6 | Human | Lung | IAC | 2.37e-03 | 5.05e-01 | 0.3385 |
55227 | LRRC1 | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 1.08e-04 | 3.86e-01 | -0.2116 |
55227 | LRRC1 | C04 | Human | Oral cavity | OSCC | 8.82e-05 | 3.72e-01 | 0.2633 |
55227 | LRRC1 | C21 | Human | Oral cavity | OSCC | 2.22e-13 | 5.30e-01 | 0.2678 |
55227 | LRRC1 | C30 | Human | Oral cavity | OSCC | 4.84e-13 | 5.84e-01 | 0.3055 |
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Transcriptomic changes along malignancy continuum. |
∗log2FC in expression of this searched gene in stem-like cells from each diseased tissue sample relative to stem-like cells in normal samples in each tissue plotted against the malignancy continuum. Samples are colored based on if they are from different disease stage. |
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Malignant transformation related pathway analysis |
Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
Figure of enriched GO biological processes. |
Tissue | Disease Stage | Enriched GO biological Processes |
Colorectum | AD | |
Colorectum | SER | |
Colorectum | MSS | |
Colorectum | MSI-H | |
Colorectum | FAP |
∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0044403 | Colorectum | AD | biological process involved in symbiotic interaction | 99/3918 | 290/18723 | 1.02e-07 | 4.93e-06 | 99 |
GO:0048872 | Colorectum | AD | homeostasis of number of cells | 87/3918 | 272/18723 | 1.16e-05 | 2.61e-04 | 87 |
GO:0035821 | Colorectum | AD | modulation of process of other organism | 34/3918 | 106/18723 | 4.73e-03 | 3.22e-02 | 34 |
GO:00444032 | Colorectum | MSS | biological process involved in symbiotic interaction | 93/3467 | 290/18723 | 1.72e-08 | 9.85e-07 | 93 |
GO:00488722 | Colorectum | MSS | homeostasis of number of cells | 82/3467 | 272/18723 | 2.02e-06 | 6.28e-05 | 82 |
GO:00358211 | Colorectum | MSS | modulation of process of other organism | 33/3467 | 106/18723 | 1.18e-03 | 1.14e-02 | 33 |
GO:0002221 | Colorectum | MSS | pattern recognition receptor signaling pathway | 45/3467 | 172/18723 | 8.06e-03 | 4.91e-02 | 45 |
GO:00444034 | Colorectum | FAP | biological process involved in symbiotic interaction | 66/2622 | 290/18723 | 3.47e-05 | 7.64e-04 | 66 |
GO:00488724 | Colorectum | FAP | homeostasis of number of cells | 60/2622 | 272/18723 | 1.91e-04 | 2.79e-03 | 60 |
GO:00444035 | Colorectum | CRC | biological process involved in symbiotic interaction | 55/2078 | 290/18723 | 4.82e-05 | 1.12e-03 | 55 |
GO:00488725 | Colorectum | CRC | homeostasis of number of cells | 48/2078 | 272/18723 | 7.78e-04 | 9.87e-03 | 48 |
GO:00510908 | Esophagus | ESCC | regulation of DNA-binding transcription factor activity | 252/8552 | 440/18723 | 5.22e-07 | 6.97e-06 | 252 |
GO:00434332 | Esophagus | ESCC | negative regulation of DNA-binding transcription factor activity | 103/8552 | 185/18723 | 3.86e-03 | 1.57e-02 | 103 |
GO:00320882 | Esophagus | ESCC | negative regulation of NF-kappaB transcription factor activity | 54/8552 | 93/18723 | 1.08e-02 | 3.67e-02 | 54 |
GO:00022211 | Liver | HCC | pattern recognition receptor signaling pathway | 107/7958 | 172/18723 | 1.37e-07 | 2.58e-06 | 107 |
GO:00510902 | Liver | HCC | regulation of DNA-binding transcription factor activity | 220/7958 | 440/18723 | 8.04e-04 | 4.82e-03 | 220 |
GO:0002224 | Liver | HCC | toll-like receptor signaling pathway | 67/7958 | 121/18723 | 2.87e-03 | 1.34e-02 | 67 |
GO:00622072 | Liver | HCC | regulation of pattern recognition receptor signaling pathway | 59/7958 | 105/18723 | 3.18e-03 | 1.47e-02 | 59 |
GO:00510907 | Oral cavity | OSCC | regulation of DNA-binding transcription factor activity | 221/7305 | 440/18723 | 9.06e-07 | 1.23e-05 | 221 |
GO:00022214 | Oral cavity | OSCC | pattern recognition receptor signaling pathway | 95/7305 | 172/18723 | 1.11e-05 | 1.15e-04 | 95 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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Cell-cell communication analysis |
Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
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Somatic mutation of malignant transformation related genes |
Annotation of somatic variants for genes involved in malignant transformation |
Hugo Symbol | Variant Class | Variant Classification | dbSNP RS | HGVSc | HGVSp | HGVSp Short | SWISSPROT | BIOTYPE | SIFT | PolyPhen | Tumor Sample Barcode | Tissue | Histology | Sex | Age | Stage | Therapy Types | Drugs | Outcome |
LRRC1 | SNV | Missense_Mutation | novel | c.401C>T | p.Ser134Phe | p.S134F | Q9BTT6 | protein_coding | tolerated(0.64) | probably_damaging(0.996) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LRRC1 | SNV | Missense_Mutation | c.731N>T | p.Ser244Leu | p.S244L | Q9BTT6 | protein_coding | tolerated(0.21) | possibly_damaging(0.489) | TCGA-C8-A275-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
LRRC1 | SNV | Missense_Mutation | c.1066C>G | p.Gln356Glu | p.Q356E | Q9BTT6 | protein_coding | tolerated(0.13) | benign(0.079) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD | |
LRRC1 | SNV | Missense_Mutation | c.484C>T | p.Leu162Phe | p.L162F | Q9BTT6 | protein_coding | deleterious(0.03) | possibly_damaging(0.864) | TCGA-EK-A2PM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
LRRC1 | SNV | Missense_Mutation | c.1568N>T | p.Ser523Phe | p.S523F | Q9BTT6 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.991) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
LRRC1 | insertion | Frame_Shift_Ins | novel | c.625_626insT | p.Ser210ValfsTer20 | p.S210Vfs*20 | Q9BTT6 | protein_coding | TCGA-ZJ-AAXB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | ||
LRRC1 | SNV | Missense_Mutation | novel | c.1433N>C | p.Arg478Pro | p.R478P | Q9BTT6 | protein_coding | deleterious(0.01) | possibly_damaging(0.6) | TCGA-AA-3877-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LRRC1 | SNV | Missense_Mutation | novel | c.1055C>T | p.Ala352Val | p.A352V | Q9BTT6 | protein_coding | tolerated(0.13) | benign(0.01) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
LRRC1 | SNV | Missense_Mutation | rs751741483 | c.272N>A | p.Arg91Gln | p.R91Q | Q9BTT6 | protein_coding | deleterious(0.02) | probably_damaging(0.997) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LRRC1 | SNV | Missense_Mutation | rs774261475 | c.1370C>T | p.Ala457Val | p.A457V | Q9BTT6 | protein_coding | tolerated(1) | benign(0.007) | TCGA-AM-5821-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
Identification of chemicals and drugs interact with genes involved in malignant transfromation |
(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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