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Gene: LYST |
Gene summary for LYST |
Gene summary. |
Gene information | Species | Human | Gene symbol | LYST | Gene ID | 1130 |
Gene name | lysosomal trafficking regulator | |
Gene Alias | CHS | |
Cytomap | 1q42.3 | |
Gene Type | protein-coding | GO ID | GO:0001562 | UniProtAcc | Q99698 |
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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 |
1130 | LYST | P128T-E | Human | Esophagus | ESCC | 1.05e-06 | 2.91e-01 | 0.1241 |
1130 | LYST | P130T-E | Human | Esophagus | ESCC | 2.99e-37 | 7.88e-01 | 0.1676 |
1130 | LYST | NAFLD1 | Human | Liver | NAFLD | 7.57e-05 | 5.53e-01 | -0.04 |
1130 | LYST | HCC1_Meng | Human | Liver | HCC | 4.67e-07 | -1.60e-01 | 0.0246 |
1130 | LYST | HCC2_Meng | Human | Liver | HCC | 1.16e-08 | -4.14e-02 | 0.0107 |
1130 | LYST | HCC1 | Human | Liver | HCC | 1.35e-04 | 3.18e+00 | 0.5336 |
1130 | LYST | HCC2 | Human | Liver | HCC | 7.01e-12 | 2.66e+00 | 0.5341 |
1130 | LYST | HCC5 | Human | Liver | HCC | 8.46e-05 | 2.31e+00 | 0.4932 |
1130 | LYST | S028 | Human | Liver | HCC | 1.98e-03 | 4.43e-01 | 0.2503 |
1130 | LYST | S029 | Human | Liver | HCC | 1.58e-04 | 4.93e-01 | 0.2581 |
1130 | LYST | RNA-P17T-P17T-2 | Human | Lung | IAC | 1.36e-04 | 5.32e-01 | 0.3371 |
1130 | LYST | RNA-P17T-P17T-4 | Human | Lung | IAC | 1.58e-04 | 6.20e-01 | 0.343 |
1130 | LYST | RNA-P17T-P17T-8 | Human | Lung | IAC | 1.29e-05 | 5.23e-01 | 0.3329 |
1130 | LYST | RNA-P25T1-P25T1-1 | Human | Lung | AIS | 5.51e-05 | 4.02e-01 | -0.2116 |
1130 | LYST | RNA-P6T2-P6T2-1 | Human | Lung | IAC | 7.96e-11 | 4.56e-01 | -0.0166 |
1130 | LYST | RNA-P6T2-P6T2-2 | Human | Lung | IAC | 1.37e-16 | 4.93e-01 | -0.0132 |
1130 | LYST | RNA-P6T2-P6T2-3 | Human | Lung | IAC | 7.04e-23 | 5.87e-01 | -0.013 |
1130 | LYST | RNA-P6T2-P6T2-4 | Human | Lung | IAC | 2.60e-09 | 4.61e-01 | -0.0121 |
1130 | LYST | C04 | Human | Oral cavity | OSCC | 1.61e-10 | 6.96e-01 | 0.2633 |
1130 | LYST | C21 | Human | Oral cavity | OSCC | 4.43e-12 | 5.19e-01 | 0.2678 |
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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:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
GO:001619715 | Esophagus | ESCC | endosomal transport | 168/8552 | 230/18723 | 2.28e-17 | 1.93e-15 | 168 |
GO:000703417 | Esophagus | ESCC | vacuolar transport | 119/8552 | 157/18723 | 1.16e-14 | 6.30e-13 | 119 |
GO:000961518 | Esophagus | ESCC | response to virus | 238/8552 | 367/18723 | 6.65e-14 | 3.32e-12 | 238 |
GO:000703314 | Esophagus | ESCC | vacuole organization | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
GO:00516075 | Esophagus | ESCC | defense response to virus | 171/8552 | 265/18723 | 3.91e-10 | 1.05e-08 | 171 |
GO:01405465 | Esophagus | ESCC | defense response to symbiont | 171/8552 | 265/18723 | 3.91e-10 | 1.05e-08 | 171 |
GO:007198514 | Esophagus | ESCC | multivesicular body sorting pathway | 34/8552 | 37/18723 | 3.49e-09 | 7.39e-08 | 34 |
GO:00070419 | Esophagus | ESCC | lysosomal transport | 83/8552 | 114/18723 | 3.52e-09 | 7.41e-08 | 83 |
GO:003250915 | Esophagus | ESCC | endosome transport via multivesicular body sorting pathway | 29/8552 | 31/18723 | 1.92e-08 | 3.72e-07 | 29 |
GO:00070403 | Esophagus | ESCC | lysosome organization | 53/8552 | 74/18723 | 5.34e-06 | 5.57e-05 | 53 |
GO:00801713 | Esophagus | ESCC | lytic vacuole organization | 53/8552 | 74/18723 | 5.34e-06 | 5.57e-05 | 53 |
GO:00330593 | Esophagus | ESCC | cellular pigmentation | 40/8552 | 53/18723 | 9.67e-06 | 9.21e-05 | 40 |
GO:00083333 | Esophagus | ESCC | endosome to lysosome transport | 40/8552 | 55/18723 | 4.27e-05 | 3.42e-04 | 40 |
GO:00487531 | Esophagus | ESCC | pigment granule organization | 23/8552 | 29/18723 | 2.25e-04 | 1.40e-03 | 23 |
GO:00324381 | Esophagus | ESCC | melanosome organization | 22/8552 | 28/18723 | 3.95e-04 | 2.26e-03 | 22 |
GO:00434731 | Esophagus | ESCC | pigmentation | 59/8552 | 98/18723 | 2.64e-03 | 1.12e-02 | 59 |
GO:00161975 | Liver | NAFLD | endosomal transport | 41/1882 | 230/18723 | 2.02e-04 | 3.53e-03 | 41 |
GO:00160505 | Liver | NAFLD | vesicle organization | 50/1882 | 300/18723 | 2.42e-04 | 4.06e-03 | 50 |
GO:00070345 | Liver | NAFLD | vacuolar transport | 28/1882 | 157/18723 | 1.91e-03 | 1.93e-02 | 28 |
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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 |
LYST | SNV | Missense_Mutation | novel | c.825N>C | p.Leu275Phe | p.L275F | Q99698 | protein_coding | deleterious(0.02) | possibly_damaging(0.894) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
LYST | SNV | Missense_Mutation | novel | c.10055N>C | p.Gln3352Pro | p.Q3352P | Q99698 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A2-A04T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
LYST | SNV | Missense_Mutation | c.3283N>A | p.Glu1095Lys | p.E1095K | Q99698 | protein_coding | deleterious(0) | benign(0.219) | TCGA-A2-A0CT-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cytoxan | SD | |
LYST | SNV | Missense_Mutation | c.5230N>T | p.Val1744Phe | p.V1744F | Q99698 | protein_coding | deleterious(0.01) | possibly_damaging(0.646) | TCGA-A2-A0T1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Targeted Molecular therapy | herceptin | SD | |
LYST | SNV | Missense_Mutation | c.9136A>G | p.Asn3046Asp | p.N3046D | Q99698 | protein_coding | tolerated(0.14) | benign(0.351) | TCGA-A2-A25E-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | PD | |
LYST | SNV | Missense_Mutation | novel | c.5273N>A | p.Pro1758Gln | p.P1758Q | Q99698 | protein_coding | deleterious(0.05) | probably_damaging(0.999) | TCGA-A7-A3RF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD |
LYST | SNV | Missense_Mutation | c.9839N>C | p.Arg3280Pro | p.R3280P | Q99698 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A8-A07R-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Ancillary | zoledronic | SD | |
LYST | SNV | Missense_Mutation | c.9475G>A | p.Asp3159Asn | p.D3159N | Q99698 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
LYST | SNV | Missense_Mutation | c.3310C>G | p.Arg1104Gly | p.R1104G | Q99698 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
LYST | SNV | Missense_Mutation | novel | c.6861N>A | p.Asn2287Lys | p.N2287K | Q99698 | protein_coding | tolerated(0.92) | benign(0) | TCGA-AC-A2FO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | chemo | 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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