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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 | LZE4T | Human | Esophagus | ESCC | 2.88e-12 | 4.21e-01 | 0.0811 |
1130 | LYST | LZE7T | Human | Esophagus | ESCC | 1.54e-02 | 1.52e-01 | 0.0667 |
1130 | LYST | LZE8T | Human | Esophagus | ESCC | 3.54e-04 | 1.39e-01 | 0.067 |
1130 | LYST | LZE20T | Human | Esophagus | ESCC | 1.94e-03 | 1.03e-01 | 0.0662 |
1130 | LYST | LZE24T | Human | Esophagus | ESCC | 4.74e-08 | 1.78e-01 | 0.0596 |
1130 | LYST | LZE21T | Human | Esophagus | ESCC | 2.09e-02 | 1.92e-01 | 0.0655 |
1130 | LYST | LZE6T | Human | Esophagus | ESCC | 1.10e-04 | 1.74e-01 | 0.0845 |
1130 | LYST | P1T-E | Human | Esophagus | ESCC | 4.77e-03 | 8.41e-02 | 0.0875 |
1130 | LYST | P2T-E | Human | Esophagus | ESCC | 1.57e-37 | 7.56e-01 | 0.1177 |
1130 | LYST | P4T-E | Human | Esophagus | ESCC | 4.33e-03 | 1.42e-01 | 0.1323 |
1130 | LYST | P5T-E | Human | Esophagus | ESCC | 5.50e-18 | 5.48e-01 | 0.1327 |
1130 | LYST | P8T-E | Human | Esophagus | ESCC | 3.98e-04 | 1.31e-01 | 0.0889 |
1130 | LYST | P9T-E | Human | Esophagus | ESCC | 1.40e-17 | 2.83e-01 | 0.1131 |
1130 | LYST | P10T-E | Human | Esophagus | ESCC | 1.15e-19 | 2.68e-01 | 0.116 |
1130 | LYST | P11T-E | Human | Esophagus | ESCC | 4.95e-14 | 6.02e-01 | 0.1426 |
1130 | LYST | P12T-E | Human | Esophagus | ESCC | 2.10e-03 | 1.68e-01 | 0.1122 |
1130 | LYST | P15T-E | Human | Esophagus | ESCC | 3.67e-08 | 2.18e-01 | 0.1149 |
1130 | LYST | P16T-E | Human | Esophagus | ESCC | 2.40e-63 | 1.35e+00 | 0.1153 |
1130 | LYST | P19T-E | Human | Esophagus | ESCC | 3.09e-03 | 1.56e-01 | 0.1662 |
1130 | LYST | P20T-E | Human | Esophagus | ESCC | 1.79e-10 | 1.29e-01 | 0.1124 |
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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 | c.5177N>G | p.Phe1726Cys | p.F1726C | Q99698 | protein_coding | deleterious(0) | possibly_damaging(0.885) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
LYST | SNV | Missense_Mutation | rs550465065 | c.1526N>G | p.Phe509Cys | p.F509C | Q99698 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
LYST | SNV | Missense_Mutation | c.11299N>C | p.Tyr3767His | p.Y3767H | Q99698 | protein_coding | deleterious(0) | probably_damaging(0.945) | TCGA-AA-A02W-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
LYST | SNV | Missense_Mutation | novel | c.9989N>T | p.Ala3330Val | p.A3330V | Q99698 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
LYST | SNV | Missense_Mutation | c.9461N>A | p.Gly3154Asp | p.G3154D | Q99698 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AD-6895-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
LYST | SNV | Missense_Mutation | c.3323C>T | p.Ala1108Val | p.A1108V | Q99698 | protein_coding | deleterious(0) | benign(0.419) | TCGA-AD-6964-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folfox | PD | |
LYST | SNV | Missense_Mutation | c.10697N>G | p.Tyr3566Cys | p.Y3566C | Q99698 | protein_coding | deleterious(0.01) | possibly_damaging(0.708) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
LYST | SNV | Missense_Mutation | novel | c.8115T>G | p.Ile2705Met | p.I2705M | Q99698 | protein_coding | tolerated(1) | benign(0) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
LYST | SNV | Missense_Mutation | novel | c.3119C>A | p.Ser1040Tyr | p.S1040Y | Q99698 | protein_coding | tolerated_low_confidence(0.07) | benign(0.047) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
LYST | SNV | Missense_Mutation | novel | c.2236N>A | p.Ala746Thr | p.A746T | Q99698 | protein_coding | tolerated(0.22) | benign(0.172) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | 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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