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Gene: LRCH3 |
Gene summary for LRCH3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LRCH3 | Gene ID | 84859 |
Gene name | leucine rich repeats and calponin homology domain containing 3 | |
Gene Alias | LRCH3 | |
Cytomap | 3q29 | |
Gene Type | protein-coding | GO ID | GO:0006996 | UniProtAcc | B4DU23 |
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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 |
84859 | LRCH3 | CCI_1 | Human | Cervix | CC | 2.53e-04 | 5.96e-01 | 0.528 |
84859 | LRCH3 | CCI_2 | Human | Cervix | CC | 5.73e-12 | 1.15e+00 | 0.5249 |
84859 | LRCH3 | CCI_3 | Human | Cervix | CC | 5.83e-20 | 9.76e-01 | 0.516 |
84859 | LRCH3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 3.39e-05 | 5.55e-01 | -0.0811 |
84859 | LRCH3 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.21e-16 | 6.89e-01 | -0.1954 |
84859 | LRCH3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.96e-06 | 5.25e-01 | -0.059 |
84859 | LRCH3 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.03e-04 | 5.39e-01 | 0.0588 |
84859 | LRCH3 | A002-C-010 | Human | Colorectum | FAP | 7.04e-03 | -1.22e-01 | 0.242 |
84859 | LRCH3 | A015-C-203 | Human | Colorectum | FAP | 2.93e-23 | -3.28e-01 | -0.1294 |
84859 | LRCH3 | A015-C-204 | Human | Colorectum | FAP | 1.98e-04 | -2.92e-01 | -0.0228 |
84859 | LRCH3 | A002-C-201 | Human | Colorectum | FAP | 1.73e-08 | -2.89e-01 | 0.0324 |
84859 | LRCH3 | A002-C-203 | Human | Colorectum | FAP | 6.94e-04 | -1.51e-01 | 0.2786 |
84859 | LRCH3 | A001-C-108 | Human | Colorectum | FAP | 1.49e-15 | -1.89e-01 | -0.0272 |
84859 | LRCH3 | A002-C-205 | Human | Colorectum | FAP | 2.05e-14 | -1.98e-01 | -0.1236 |
84859 | LRCH3 | A015-C-006 | Human | Colorectum | FAP | 1.15e-08 | -2.53e-01 | -0.0994 |
84859 | LRCH3 | A015-C-106 | Human | Colorectum | FAP | 1.30e-10 | -2.28e-01 | -0.0511 |
84859 | LRCH3 | A002-C-114 | Human | Colorectum | FAP | 1.71e-12 | -3.91e-01 | -0.1561 |
84859 | LRCH3 | A015-C-104 | Human | Colorectum | FAP | 2.86e-24 | -2.77e-01 | -0.1899 |
84859 | LRCH3 | A001-C-014 | Human | Colorectum | FAP | 8.32e-13 | -2.23e-01 | 0.0135 |
84859 | LRCH3 | A002-C-016 | Human | Colorectum | FAP | 8.92e-20 | -2.71e-01 | 0.0521 |
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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 |
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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 |
LRCH3 | SNV | Missense_Mutation | novel | c.167N>T | p.Ala56Val | p.A56V | Q96II8 | protein_coding | deleterious(0) | probably_damaging(0.937) | TCGA-3C-AALJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
LRCH3 | SNV | Missense_Mutation | c.1246N>T | p.His416Tyr | p.H416Y | Q96II8 | protein_coding | tolerated(0.73) | benign(0.263) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
LRCH3 | SNV | Missense_Mutation | rs754369527 | c.1046N>A | p.Arg349Gln | p.R349Q | Q96II8 | protein_coding | deleterious(0.05) | probably_damaging(0.926) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LRCH3 | SNV | Missense_Mutation | c.692C>T | p.Thr231Ile | p.T231I | Q96II8 | protein_coding | deleterious(0.03) | possibly_damaging(0.549) | TCGA-AR-A24Q-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
LRCH3 | SNV | Missense_Mutation | novel | c.677N>T | p.Ser226Leu | p.S226L | Q96II8 | protein_coding | deleterious(0) | benign(0.206) | TCGA-AR-A255-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | trastuzumab | SD |
LRCH3 | SNV | Missense_Mutation | c.430N>T | p.Pro144Ser | p.P144S | Q96II8 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
LRCH3 | deletion | Frame_Shift_Del | c.802_809delNNNNNNNN | p.Phe269ProfsTer7 | p.F269Pfs*7 | Q96II8 | protein_coding | TCGA-AN-A0XN-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |||
LRCH3 | deletion | Frame_Shift_Del | c.794_795delAA | p.Lys265SerfsTer5 | p.K265Sfs*5 | Q96II8 | protein_coding | TCGA-D8-A27I-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adrimycin+cyclophosphamide | SD | |||
LRCH3 | deletion | Frame_Shift_Del | novel | c.2108delN | p.His704MetfsTer7 | p.H704Mfs*7 | Q96II8 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
LRCH3 | SNV | Missense_Mutation | novel | c.1102G>T | p.Val368Leu | p.V368L | Q96II8 | protein_coding | tolerated(0.32) | benign(0.015) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
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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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