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Gene: HPS4 |
Gene summary for HPS4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | HPS4 | Gene ID | 89781 |
| Gene name | HPS4 biogenesis of lysosomal organelles complex 3 subunit 2 | |
| Gene Alias | BLOC3S2 | |
| Cytomap | 22q12.1 | |
| Gene Type | protein-coding | GO ID | GO:0006605 | UniProtAcc | A8K2E6 |
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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 |
| 89781 | HPS4 | LZE4T | Human | Esophagus | ESCC | 1.03e-09 | 2.65e-01 | 0.0811 |
| 89781 | HPS4 | LZE7T | Human | Esophagus | ESCC | 7.55e-10 | 3.94e-01 | 0.0667 |
| 89781 | HPS4 | LZE8T | Human | Esophagus | ESCC | 1.07e-03 | 1.48e-01 | 0.067 |
| 89781 | HPS4 | LZE20T | Human | Esophagus | ESCC | 1.66e-07 | 2.09e-01 | 0.0662 |
| 89781 | HPS4 | LZE24T | Human | Esophagus | ESCC | 1.94e-19 | 4.09e-01 | 0.0596 |
| 89781 | HPS4 | LZE21T | Human | Esophagus | ESCC | 9.90e-05 | 3.77e-01 | 0.0655 |
| 89781 | HPS4 | LZE6T | Human | Esophagus | ESCC | 1.19e-03 | 1.68e-01 | 0.0845 |
| 89781 | HPS4 | P1T-E | Human | Esophagus | ESCC | 2.78e-09 | 4.11e-01 | 0.0875 |
| 89781 | HPS4 | P2T-E | Human | Esophagus | ESCC | 1.20e-34 | 5.81e-01 | 0.1177 |
| 89781 | HPS4 | P4T-E | Human | Esophagus | ESCC | 3.27e-13 | 3.23e-01 | 0.1323 |
| 89781 | HPS4 | P5T-E | Human | Esophagus | ESCC | 1.87e-07 | 1.61e-01 | 0.1327 |
| 89781 | HPS4 | P8T-E | Human | Esophagus | ESCC | 6.65e-17 | 3.09e-01 | 0.0889 |
| 89781 | HPS4 | P9T-E | Human | Esophagus | ESCC | 3.34e-13 | 2.86e-01 | 0.1131 |
| 89781 | HPS4 | P10T-E | Human | Esophagus | ESCC | 1.56e-40 | 7.41e-01 | 0.116 |
| 89781 | HPS4 | P11T-E | Human | Esophagus | ESCC | 3.35e-12 | 5.33e-01 | 0.1426 |
| 89781 | HPS4 | P12T-E | Human | Esophagus | ESCC | 2.44e-25 | 4.13e-01 | 0.1122 |
| 89781 | HPS4 | P15T-E | Human | Esophagus | ESCC | 3.91e-22 | 4.47e-01 | 0.1149 |
| 89781 | HPS4 | P16T-E | Human | Esophagus | ESCC | 2.21e-47 | 7.02e-01 | 0.1153 |
| 89781 | HPS4 | P17T-E | Human | Esophagus | ESCC | 3.81e-07 | 3.49e-01 | 0.1278 |
| 89781 | HPS4 | P20T-E | Human | Esophagus | ESCC | 1.63e-12 | 2.61e-01 | 0.1124 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:0072594110 | Esophagus | ESCC | establishment of protein localization to organelle | 311/8552 | 422/18723 | 3.02e-32 | 2.13e-29 | 311 |
| GO:0031647111 | Esophagus | ESCC | regulation of protein stability | 223/8552 | 298/18723 | 5.76e-25 | 1.52e-22 | 223 |
| GO:003238618 | Esophagus | ESCC | regulation of intracellular transport | 243/8552 | 337/18723 | 3.20e-23 | 7.25e-21 | 243 |
| GO:0006605111 | Esophagus | ESCC | protein targeting | 229/8552 | 314/18723 | 4.93e-23 | 1.01e-20 | 229 |
| GO:0006839110 | Esophagus | ESCC | mitochondrial transport | 187/8552 | 254/18723 | 8.35e-20 | 9.81e-18 | 187 |
| GO:1903829111 | Esophagus | ESCC | positive regulation of cellular protein localization | 199/8552 | 276/18723 | 2.99e-19 | 3.45e-17 | 199 |
| GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
| GO:0033157110 | Esophagus | ESCC | regulation of intracellular protein transport | 169/8552 | 229/18723 | 3.31e-18 | 3.23e-16 | 169 |
| GO:0032388110 | Esophagus | ESCC | positive regulation of intracellular transport | 152/8552 | 202/18723 | 7.89e-18 | 7.36e-16 | 152 |
| GO:1904951111 | Esophagus | ESCC | positive regulation of establishment of protein localization | 216/8552 | 319/18723 | 1.01e-15 | 6.86e-14 | 216 |
| GO:0072655110 | Esophagus | ESCC | establishment of protein localization to mitochondrion | 97/8552 | 120/18723 | 2.17e-15 | 1.33e-13 | 97 |
| GO:009031617 | Esophagus | ESCC | positive regulation of intracellular protein transport | 122/8552 | 160/18723 | 2.45e-15 | 1.49e-13 | 122 |
| GO:0070585110 | Esophagus | ESCC | protein localization to mitochondrion | 100/8552 | 125/18723 | 2.96e-15 | 1.77e-13 | 100 |
| GO:0050821111 | Esophagus | ESCC | protein stabilization | 140/8552 | 191/18723 | 6.50e-15 | 3.61e-13 | 140 |
| GO:0051222111 | Esophagus | ESCC | positive regulation of protein transport | 204/8552 | 303/18723 | 1.56e-14 | 8.38e-13 | 204 |
| GO:0006626110 | Esophagus | ESCC | protein targeting to mitochondrion | 81/8552 | 100/18723 | 3.60e-13 | 1.67e-11 | 81 |
| GO:000703314 | Esophagus | ESCC | vacuole organization | 127/8552 | 180/18723 | 1.04e-11 | 3.85e-10 | 127 |
| GO:004206027 | Esophagus | ESCC | wound healing | 243/8552 | 422/18723 | 4.62e-07 | 6.25e-06 | 243 |
| 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 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| HPS4 | SNV | Missense_Mutation | novel | c.1978N>T | p.Ala660Ser | p.A660S | Q9NQG7 | protein_coding | deleterious(0.02) | probably_damaging(0.986) | TCGA-A8-A08H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| HPS4 | SNV | Missense_Mutation | c.365C>A | p.Pro122His | p.P122H | Q9NQG7 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HPS4 | SNV | Missense_Mutation | c.874N>T | p.Ala292Ser | p.A292S | Q9NQG7 | protein_coding | tolerated(0.15) | benign(0.178) | TCGA-BH-A0BJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| HPS4 | SNV | Missense_Mutation | c.304N>C | p.Asp102His | p.D102H | Q9NQG7 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-BH-A0DZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | docetaxel | SD | |
| HPS4 | insertion | Nonsense_Mutation | novel | c.1411_1412insGGGGGTAAAAGC | p.Leu470_Leu471insTrpGlyTerLys | p.L470_L471insWG*K | Q9NQG7 | protein_coding | TCGA-A2-A0T2-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | xeloda | PD | ||
| HPS4 | insertion | In_Frame_Ins | novel | c.2100_2101insTCCCTTACTCTAGGTGAATGCTTCACTGCTGAGGTCCCCTCA | p.Leu700_Leu701insSerLeuThrLeuGlyGluCysPheThrAlaGluValProSer | p.L700_L701insSLTLGECFTAEVPS | Q9NQG7 | protein_coding | TCGA-BH-A0B7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR | ||
| HPS4 | SNV | Missense_Mutation | novel | c.1547N>T | p.Gln516Leu | p.Q516L | Q9NQG7 | protein_coding | tolerated(0.23) | benign(0.15) | TCGA-DS-A1OA-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |
| HPS4 | SNV | Missense_Mutation | c.1388N>A | p.Arg463Lys | p.R463K | Q9NQG7 | protein_coding | tolerated(0.33) | benign(0.058) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| HPS4 | SNV | Missense_Mutation | c.176N>C | p.Gly59Ala | p.G59A | Q9NQG7 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-EK-A2RC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| HPS4 | insertion | In_Frame_Ins | novel | c.1545_1546insTCC | p.Cys515_Gln516insSer | p.C515_Q516insS | Q9NQG7 | protein_coding | TCGA-DS-A1OA-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | carboplatin | PD |
| Page: 1 2 3 4 5 6 7 8 |
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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 |
| Page: 1 |
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