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Gene: LRRC8D |
Gene summary for LRRC8D |
Gene summary. |
Gene information | Species | Human | Gene symbol | LRRC8D | Gene ID | 55144 |
Gene name | leucine rich repeat containing 8 VRAC subunit D | |
Gene Alias | HsLRRC8D | |
Cytomap | 1p22.2 | |
Gene Type | protein-coding | GO ID | GO:0001678 | UniProtAcc | B3KRU1 |
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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 |
55144 | LRRC8D | P74T-E | Human | Esophagus | ESCC | 7.44e-13 | 3.66e-01 | 0.1479 |
55144 | LRRC8D | P75T-E | Human | Esophagus | ESCC | 3.95e-04 | 1.13e-01 | 0.1125 |
55144 | LRRC8D | P76T-E | Human | Esophagus | ESCC | 4.89e-07 | 1.75e-01 | 0.1207 |
55144 | LRRC8D | P79T-E | Human | Esophagus | ESCC | 3.56e-07 | 7.36e-02 | 0.1154 |
55144 | LRRC8D | P80T-E | Human | Esophagus | ESCC | 2.15e-18 | 5.41e-01 | 0.155 |
55144 | LRRC8D | P82T-E | Human | Esophagus | ESCC | 3.62e-05 | 1.94e-01 | 0.1072 |
55144 | LRRC8D | P83T-E | Human | Esophagus | ESCC | 8.83e-12 | 5.05e-01 | 0.1738 |
55144 | LRRC8D | P91T-E | Human | Esophagus | ESCC | 4.91e-10 | 8.25e-01 | 0.1828 |
55144 | LRRC8D | P107T-E | Human | Esophagus | ESCC | 1.15e-04 | 1.37e-01 | 0.171 |
55144 | LRRC8D | P126T-E | Human | Esophagus | ESCC | 1.36e-03 | 3.56e-01 | 0.1125 |
55144 | LRRC8D | P127T-E | Human | Esophagus | ESCC | 1.94e-17 | 2.20e-01 | 0.0826 |
55144 | LRRC8D | P128T-E | Human | Esophagus | ESCC | 4.37e-20 | 4.90e-01 | 0.1241 |
55144 | LRRC8D | P130T-E | Human | Esophagus | ESCC | 1.53e-38 | 7.00e-01 | 0.1676 |
55144 | LRRC8D | HCC1_Meng | Human | Liver | HCC | 4.44e-52 | 1.19e-01 | 0.0246 |
55144 | LRRC8D | HCC2_Meng | Human | Liver | HCC | 2.39e-06 | 3.83e-02 | 0.0107 |
55144 | LRRC8D | HCC1 | Human | Liver | HCC | 8.33e-06 | 2.95e+00 | 0.5336 |
55144 | LRRC8D | HCC2 | Human | Liver | HCC | 8.36e-03 | 1.44e+00 | 0.5341 |
55144 | LRRC8D | S014 | Human | Liver | HCC | 1.18e-09 | 3.61e-01 | 0.2254 |
55144 | LRRC8D | S015 | Human | Liver | HCC | 1.05e-15 | 5.52e-01 | 0.2375 |
55144 | LRRC8D | S016 | Human | Liver | HCC | 1.16e-13 | 4.20e-01 | 0.2243 |
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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:0062197111 | Esophagus | ESCC | cellular response to chemical stress | 234/8552 | 337/18723 | 5.37e-19 | 5.97e-17 | 234 |
GO:007121419 | Esophagus | ESCC | cellular response to abiotic stimulus | 206/8552 | 331/18723 | 7.52e-10 | 1.88e-08 | 206 |
GO:010400419 | Esophagus | ESCC | cellular response to environmental stimulus | 206/8552 | 331/18723 | 7.52e-10 | 1.88e-08 | 206 |
GO:00069707 | Esophagus | ESCC | response to osmotic stress | 57/8552 | 84/18723 | 3.26e-05 | 2.70e-04 | 57 |
GO:00714707 | Esophagus | ESCC | cellular response to osmotic stress | 31/8552 | 41/18723 | 9.32e-05 | 6.68e-04 | 31 |
GO:00512592 | Esophagus | ESCC | protein complex oligomerization | 130/8552 | 238/18723 | 3.29e-03 | 1.36e-02 | 130 |
GO:006219722 | Liver | HCC | cellular response to chemical stress | 216/7958 | 337/18723 | 6.86e-16 | 5.44e-14 | 216 |
GO:007121421 | Liver | HCC | cellular response to abiotic stimulus | 183/7958 | 331/18723 | 1.59e-06 | 2.26e-05 | 183 |
GO:010400421 | Liver | HCC | cellular response to environmental stimulus | 183/7958 | 331/18723 | 1.59e-06 | 2.26e-05 | 183 |
GO:00069702 | Liver | HCC | response to osmotic stress | 52/7958 | 84/18723 | 2.58e-04 | 1.92e-03 | 52 |
GO:004259322 | Liver | HCC | glucose homeostasis | 137/7958 | 258/18723 | 3.59e-04 | 2.49e-03 | 137 |
GO:003350022 | Liver | HCC | carbohydrate homeostasis | 137/7958 | 259/18723 | 4.45e-04 | 2.98e-03 | 137 |
GO:000167822 | Liver | HCC | cellular glucose homeostasis | 95/7958 | 172/18723 | 4.95e-04 | 3.24e-03 | 95 |
GO:00714701 | Liver | HCC | cellular response to osmotic stress | 28/7958 | 41/18723 | 7.54e-04 | 4.55e-03 | 28 |
GO:006219720 | Oral cavity | OSCC | cellular response to chemical stress | 204/7305 | 337/18723 | 6.89e-16 | 5.19e-14 | 204 |
GO:007121416 | Oral cavity | OSCC | cellular response to abiotic stimulus | 186/7305 | 331/18723 | 1.38e-10 | 4.10e-09 | 186 |
GO:010400416 | Oral cavity | OSCC | cellular response to environmental stimulus | 186/7305 | 331/18723 | 1.38e-10 | 4.10e-09 | 186 |
GO:00069706 | Oral cavity | OSCC | response to osmotic stress | 50/7305 | 84/18723 | 1.11e-04 | 8.15e-04 | 50 |
GO:0051259 | Oral cavity | OSCC | protein complex oligomerization | 121/7305 | 238/18723 | 1.29e-04 | 9.21e-04 | 121 |
GO:000167816 | Oral cavity | OSCC | cellular glucose homeostasis | 88/7305 | 172/18723 | 7.74e-04 | 4.22e-03 | 88 |
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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 |
LRRC8D | SNV | Missense_Mutation | c.296C>T | p.Ser99Phe | p.S99F | Q7L1W4 | protein_coding | tolerated(0.08) | benign(0.03) | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
LRRC8D | SNV | Missense_Mutation | c.1187C>A | p.Ser396Tyr | p.S396Y | Q7L1W4 | protein_coding | deleterious(0.02) | possibly_damaging(0.882) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
LRRC8D | SNV | Missense_Mutation | c.844N>C | p.Glu282Gln | p.E282Q | Q7L1W4 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BH-A0BF-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
LRRC8D | SNV | Missense_Mutation | rs756646478 | c.2012N>A | p.Arg671His | p.R671H | Q7L1W4 | protein_coding | tolerated(0.05) | benign(0.187) | TCGA-BH-A0GY-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyotxan | SD |
LRRC8D | SNV | Missense_Mutation | rs771012964 | c.2104A>G | p.Ile702Val | p.I702V | Q7L1W4 | protein_coding | tolerated(0.07) | possibly_damaging(0.735) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LRRC8D | insertion | In_Frame_Ins | novel | c.1408_1409insCTTTTGCCATTAAAAGTAGTGGCAAAAACTGCAATCACTTTC | p.Asp470delinsAlaPheAlaIleLysSerSerGlyLysAsnCysAsnHisPheHis | p.D470delinsAFAIKSSGKNCNHFH | Q7L1W4 | protein_coding | TCGA-A8-A09M-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | paclitaxel | CR | ||
LRRC8D | insertion | Frame_Shift_Ins | novel | c.294_295insA | p.Ser99IlefsTer10 | p.S99Ifs*10 | Q7L1W4 | protein_coding | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
LRRC8D | insertion | Frame_Shift_Ins | novel | c.294_295insATTCTAGAGA | p.Ser99IlefsTer13 | p.S99Ifs*13 | Q7L1W4 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
LRRC8D | SNV | Missense_Mutation | novel | c.1516C>T | p.Pro506Ser | p.P506S | Q7L1W4 | protein_coding | tolerated(0.21) | benign(0.035) | TCGA-C5-A8ZZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unspecific | Cisplatin | SD |
LRRC8D | SNV | Missense_Mutation | rs773687858 | c.278G>A | p.Arg93Gln | p.R93Q | Q7L1W4 | protein_coding | tolerated(0.72) | benign(0) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
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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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