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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:001605023 | Thyroid | ATC | vesicle organization | 166/6293 | 300/18723 | 6.14e-15 | 3.92e-13 | 166 |
GO:001619719 | Thyroid | ATC | endosomal transport | 128/6293 | 230/18723 | 4.44e-12 | 1.75e-10 | 128 |
GO:000703322 | Thyroid | ATC | vacuole organization | 100/6293 | 180/18723 | 1.07e-09 | 2.71e-08 | 100 |
GO:000703423 | Thyroid | ATC | vacuolar transport | 89/6293 | 157/18723 | 2.26e-09 | 5.40e-08 | 89 |
GO:0009615111 | Thyroid | ATC | response to virus | 173/6293 | 367/18723 | 4.23e-08 | 7.71e-07 | 173 |
GO:003250921 | Thyroid | ATC | endosome transport via multivesicular body sorting pathway | 25/6293 | 31/18723 | 1.01e-07 | 1.70e-06 | 25 |
GO:000704116 | Thyroid | ATC | lysosomal transport | 63/6293 | 114/18723 | 1.58e-06 | 1.93e-05 | 63 |
GO:007198515 | Thyroid | ATC | multivesicular body sorting pathway | 26/6293 | 37/18723 | 5.64e-06 | 6.00e-05 | 26 |
GO:005160712 | Thyroid | ATC | defense response to virus | 115/6293 | 265/18723 | 5.31e-04 | 3.09e-03 | 115 |
GO:014054612 | Thyroid | ATC | defense response to symbiont | 115/6293 | 265/18723 | 5.31e-04 | 3.09e-03 | 115 |
GO:000704012 | Thyroid | ATC | lysosome organization | 39/6293 | 74/18723 | 5.41e-04 | 3.13e-03 | 39 |
GO:008017112 | Thyroid | ATC | lytic vacuole organization | 39/6293 | 74/18723 | 5.41e-04 | 3.13e-03 | 39 |
GO:000833311 | Thyroid | ATC | endosome to lysosome transport | 29/6293 | 55/18723 | 2.65e-03 | 1.22e-02 | 29 |
GO:00330595 | Thyroid | ATC | cellular pigmentation | 26/6293 | 53/18723 | 1.42e-02 | 4.91e-02 | 26 |
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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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