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Gene: LRRK1 |
Gene summary for LRRK1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | LRRK1 | Gene ID | 79705 |
| Gene name | leucine rich repeat kinase 1 | |
| Gene Alias | RIPK6 | |
| Cytomap | 15q26.3 | |
| Gene Type | protein-coding | GO ID | GO:0001501 | UniProtAcc | Q38SD2 |
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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 |
| 79705 | LRRK1 | P1T-E | Human | Esophagus | ESCC | 8.58e-05 | 3.13e-01 | 0.0875 |
| 79705 | LRRK1 | P2T-E | Human | Esophagus | ESCC | 4.30e-10 | 1.78e-01 | 0.1177 |
| 79705 | LRRK1 | P4T-E | Human | Esophagus | ESCC | 2.58e-09 | 1.12e-01 | 0.1323 |
| 79705 | LRRK1 | P8T-E | Human | Esophagus | ESCC | 3.89e-12 | 2.42e-01 | 0.0889 |
| 79705 | LRRK1 | P9T-E | Human | Esophagus | ESCC | 1.10e-03 | 1.45e-01 | 0.1131 |
| 79705 | LRRK1 | P10T-E | Human | Esophagus | ESCC | 6.74e-06 | 9.30e-02 | 0.116 |
| 79705 | LRRK1 | P11T-E | Human | Esophagus | ESCC | 2.24e-05 | 1.60e-01 | 0.1426 |
| 79705 | LRRK1 | P12T-E | Human | Esophagus | ESCC | 4.31e-06 | 1.11e-01 | 0.1122 |
| 79705 | LRRK1 | P15T-E | Human | Esophagus | ESCC | 1.97e-04 | 1.06e-01 | 0.1149 |
| 79705 | LRRK1 | P16T-E | Human | Esophagus | ESCC | 1.28e-06 | 1.62e-01 | 0.1153 |
| 79705 | LRRK1 | P20T-E | Human | Esophagus | ESCC | 9.90e-05 | 9.72e-02 | 0.1124 |
| 79705 | LRRK1 | P21T-E | Human | Esophagus | ESCC | 2.05e-07 | 1.22e-01 | 0.1617 |
| 79705 | LRRK1 | P22T-E | Human | Esophagus | ESCC | 9.02e-11 | 1.77e-01 | 0.1236 |
| 79705 | LRRK1 | P23T-E | Human | Esophagus | ESCC | 1.07e-12 | 3.13e-01 | 0.108 |
| 79705 | LRRK1 | P24T-E | Human | Esophagus | ESCC | 7.90e-03 | 9.89e-02 | 0.1287 |
| 79705 | LRRK1 | P26T-E | Human | Esophagus | ESCC | 1.78e-03 | 9.65e-02 | 0.1276 |
| 79705 | LRRK1 | P27T-E | Human | Esophagus | ESCC | 5.05e-04 | 5.94e-02 | 0.1055 |
| 79705 | LRRK1 | P28T-E | Human | Esophagus | ESCC | 3.75e-03 | 8.70e-02 | 0.1149 |
| 79705 | LRRK1 | P30T-E | Human | Esophagus | ESCC | 1.10e-05 | 1.85e-01 | 0.137 |
| 79705 | LRRK1 | P32T-E | Human | Esophagus | ESCC | 7.90e-03 | 7.41e-02 | 0.1666 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias |
| ∗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:0010563111 | Esophagus | ESCC | negative regulation of phosphorus metabolic process | 274/8552 | 442/18723 | 2.32e-12 | 9.41e-11 | 274 |
| GO:0045936111 | Esophagus | ESCC | negative regulation of phosphate metabolic process | 273/8552 | 441/18723 | 3.18e-12 | 1.25e-10 | 273 |
| GO:0042326111 | Esophagus | ESCC | negative regulation of phosphorylation | 237/8552 | 385/18723 | 1.86e-10 | 5.33e-09 | 237 |
| GO:001605517 | Esophagus | ESCC | Wnt signaling pathway | 268/8552 | 444/18723 | 2.32e-10 | 6.58e-09 | 268 |
| GO:019873817 | Esophagus | ESCC | cell-cell signaling by wnt | 269/8552 | 446/18723 | 2.41e-10 | 6.79e-09 | 269 |
| GO:0001933111 | Esophagus | ESCC | negative regulation of protein phosphorylation | 213/8552 | 342/18723 | 3.54e-10 | 9.76e-09 | 213 |
| GO:0030099111 | Esophagus | ESCC | myeloid cell differentiation | 232/8552 | 381/18723 | 1.22e-09 | 2.90e-08 | 232 |
| GO:001631110 | Esophagus | ESCC | dephosphorylation | 251/8552 | 417/18723 | 1.26e-09 | 2.99e-08 | 251 |
| GO:000647018 | Esophagus | ESCC | protein dephosphorylation | 177/8552 | 281/18723 | 3.13e-09 | 6.72e-08 | 177 |
| GO:003011117 | Esophagus | ESCC | regulation of Wnt signaling pathway | 194/8552 | 328/18723 | 5.39e-07 | 7.14e-06 | 194 |
| GO:006007016 | Esophagus | ESCC | canonical Wnt signaling pathway | 180/8552 | 303/18723 | 9.15e-07 | 1.17e-05 | 180 |
| GO:006082817 | Esophagus | ESCC | regulation of canonical Wnt signaling pathway | 153/8552 | 253/18723 | 1.38e-06 | 1.67e-05 | 153 |
| GO:000257317 | Esophagus | ESCC | myeloid leukocyte differentiation | 128/8552 | 208/18723 | 2.75e-06 | 3.15e-05 | 128 |
| GO:009026316 | Esophagus | ESCC | positive regulation of canonical Wnt signaling pathway | 69/8552 | 106/18723 | 4.22e-05 | 3.39e-04 | 69 |
| GO:003017716 | Esophagus | ESCC | positive regulation of Wnt signaling pathway | 87/8552 | 140/18723 | 6.18e-05 | 4.73e-04 | 87 |
| GO:00507322 | Esophagus | ESCC | negative regulation of peptidyl-tyrosine phosphorylation | 42/8552 | 59/18723 | 6.35e-05 | 4.84e-04 | 42 |
| GO:00182124 | Esophagus | ESCC | peptidyl-tyrosine modification | 202/8552 | 378/18723 | 1.34e-03 | 6.39e-03 | 202 |
| GO:00181084 | Esophagus | ESCC | peptidyl-tyrosine phosphorylation | 200/8552 | 375/18723 | 1.60e-03 | 7.45e-03 | 200 |
| GO:00603485 | Esophagus | ESCC | bone development | 115/8552 | 205/18723 | 1.67e-03 | 7.72e-03 | 115 |
| GO:00507303 | Esophagus | ESCC | regulation of peptidyl-tyrosine phosphorylation | 144/8552 | 264/18723 | 2.22e-03 | 9.78e-03 | 144 |
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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 |
| LRRK1 | SNV | Missense_Mutation | novel | c.2907N>C | p.Glu969Asp | p.E969D | Q38SD2 | protein_coding | tolerated(0.06) | possibly_damaging(0.708) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| LRRK1 | SNV | Missense_Mutation | novel | c.3976N>T | p.Ser1326Cys | p.S1326C | Q38SD2 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-A2-A4RW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| LRRK1 | SNV | Missense_Mutation | novel | c.376N>T | p.Val126Leu | p.V126L | Q38SD2 | protein_coding | tolerated(0.8) | benign(0.007) | TCGA-A8-A07J-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
| LRRK1 | SNV | Missense_Mutation | c.622N>C | p.Asp208His | p.D208H | Q38SD2 | protein_coding | deleterious(0) | possibly_damaging(0.751) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| LRRK1 | SNV | Missense_Mutation | c.2272C>T | p.His758Tyr | p.H758Y | Q38SD2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A8-A092-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | CR | |
| LRRK1 | SNV | Missense_Mutation | c.5768G>T | p.Arg1923Met | p.R1923M | Q38SD2 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LRRK1 | SNV | Missense_Mutation | novel | c.884N>T | p.Ser295Leu | p.S295L | Q38SD2 | protein_coding | deleterious(0) | probably_damaging(0.944) | TCGA-AC-A3W6-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| LRRK1 | SNV | Missense_Mutation | c.5024A>G | p.Asn1675Ser | p.N1675S | Q38SD2 | protein_coding | deleterious(0.01) | probably_damaging(0.985) | TCGA-AN-A03Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| LRRK1 | SNV | Missense_Mutation | rs753053998 | c.2300N>A | p.Arg767His | p.R767H | Q38SD2 | protein_coding | deleterious(0.01) | probably_damaging(0.976) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| LRRK1 | SNV | Missense_Mutation | c.2217G>C | p.Trp739Cys | p.W739C | Q38SD2 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AR-A0TT-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | doxorubicin | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
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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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