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Gene: LRRC19 |
Gene summary for LRRC19 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LRRC19 | Gene ID | 64922 |
| Gene name | leucine rich repeat containing 19 | |
| Gene Alias | LRRC19 | |
| Cytomap | 9p21.2 | |
| Gene Type | protein-coding | GO ID | GO:0001816 | UniProtAcc | Q9H756 |
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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 |
| 64922 | LRRC19 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.02e-18 | 5.67e-01 | -0.1954 |
| 64922 | LRRC19 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.79e-02 | -2.07e-01 | 0.3859 |
| 64922 | LRRC19 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.08e-06 | -2.54e-01 | 0.3005 |
| 64922 | LRRC19 | A002-C-010 | Human | Colorectum | FAP | 2.55e-02 | -1.56e-01 | 0.242 |
| 64922 | LRRC19 | A015-C-203 | Human | Colorectum | FAP | 1.74e-07 | -2.05e-01 | -0.1294 |
| 64922 | LRRC19 | A002-C-201 | Human | Colorectum | FAP | 6.10e-05 | -2.57e-01 | 0.0324 |
| 64922 | LRRC19 | A001-C-119 | Human | Colorectum | FAP | 2.42e-02 | -2.50e-01 | -0.1557 |
| 64922 | LRRC19 | A001-C-108 | Human | Colorectum | FAP | 1.42e-06 | -2.00e-01 | -0.0272 |
| 64922 | LRRC19 | A002-C-205 | Human | Colorectum | FAP | 5.00e-05 | -2.51e-01 | -0.1236 |
| 64922 | LRRC19 | A001-C-104 | Human | Colorectum | FAP | 2.05e-02 | -1.82e-01 | 0.0184 |
| 64922 | LRRC19 | A015-C-006 | Human | Colorectum | FAP | 9.64e-03 | -2.58e-01 | -0.0994 |
| 64922 | LRRC19 | A015-C-106 | Human | Colorectum | FAP | 1.03e-03 | -1.84e-01 | -0.0511 |
| 64922 | LRRC19 | A002-C-114 | Human | Colorectum | FAP | 2.25e-04 | -2.59e-01 | -0.1561 |
| 64922 | LRRC19 | A015-C-104 | Human | Colorectum | FAP | 2.47e-08 | -2.43e-01 | -0.1899 |
| 64922 | LRRC19 | A001-C-014 | Human | Colorectum | FAP | 4.69e-06 | -1.96e-01 | 0.0135 |
| 64922 | LRRC19 | A002-C-016 | Human | Colorectum | FAP | 1.77e-05 | -1.85e-01 | 0.0521 |
| 64922 | LRRC19 | A001-C-007 | Human | Colorectum | CRC | 4.53e-02 | -2.77e-01 | 0.1899 |
| 64922 | LRRC19 | A002-C-116 | Human | Colorectum | FAP | 2.34e-08 | -2.01e-01 | -0.0452 |
| 64922 | LRRC19 | A018-E-020 | Human | Colorectum | FAP | 3.56e-03 | -2.13e-01 | -0.2034 |
| 64922 | LRRC19 | F034 | Human | Colorectum | FAP | 7.89e-07 | -1.88e-01 | -0.0665 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| 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 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| LRRC19 | SNV | Missense_Mutation | c.673N>A | p.Glu225Lys | p.E225K | Q9H756 | protein_coding | tolerated(0.08) | benign(0.015) | TCGA-BH-A1EV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
| LRRC19 | SNV | Missense_Mutation | novel | c.700N>A | p.Val234Ile | p.V234I | Q9H756 | protein_coding | tolerated(1) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| LRRC19 | SNV | Missense_Mutation | novel | c.581C>T | p.Ser194Leu | p.S194L | Q9H756 | protein_coding | deleterious(0) | possibly_damaging(0.543) | TCGA-C5-A8XK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| LRRC19 | SNV | Missense_Mutation | c.1006G>A | p.Glu336Lys | p.E336K | Q9H756 | protein_coding | deleterious(0.04) | benign(0.003) | TCGA-FU-A3HY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| LRRC19 | SNV | Missense_Mutation | novel | c.514A>C | p.Thr172Pro | p.T172P | Q9H756 | protein_coding | deleterious(0.01) | benign(0.26) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| LRRC19 | SNV | Missense_Mutation | c.1043N>C | p.Phe348Ser | p.F348S | Q9H756 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-QG-A5YX-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR | |
| LRRC19 | SNV | Missense_Mutation | c.298N>C | p.Glu100Gln | p.E100Q | Q9H756 | protein_coding | tolerated(0.51) | benign(0.063) | TCGA-AF-3911-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fu | PD | |
| LRRC19 | SNV | Missense_Mutation | novel | c.200N>T | p.Arg67Ile | p.R67I | Q9H756 | protein_coding | deleterious(0.05) | benign(0.009) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
| LRRC19 | insertion | Frame_Shift_Ins | novel | c.373_374insCATATAA | p.Gln125ProfsTer17 | p.Q125Pfs*17 | Q9H756 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| LRRC19 | deletion | In_Frame_Del | c.534_539delGAACTG | p.Trp178_Asn179del | p.W178_N179del | Q9H756 | protein_coding | TCGA-CK-6746-01 | 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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