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Gene: PLEKHM1 |
Gene summary for PLEKHM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PLEKHM1 | Gene ID | 9842 |
| Gene name | pleckstrin homology and RUN domain containing M1 | |
| Gene Alias | AP162 | |
| Cytomap | 17q21.31 | |
| Gene Type | protein-coding | GO ID | GO:0001894 | UniProtAcc | Q9Y4G2 |
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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 |
| 9842 | PLEKHM1 | LZE4T | Human | Esophagus | ESCC | 3.14e-07 | 2.08e-01 | 0.0811 |
| 9842 | PLEKHM1 | LZE7T | Human | Esophagus | ESCC | 1.78e-02 | 1.79e-01 | 0.0667 |
| 9842 | PLEKHM1 | LZE20T | Human | Esophagus | ESCC | 2.77e-02 | 1.19e-01 | 0.0662 |
| 9842 | PLEKHM1 | LZE22T | Human | Esophagus | ESCC | 3.68e-04 | 3.81e-01 | 0.068 |
| 9842 | PLEKHM1 | LZE24T | Human | Esophagus | ESCC | 3.89e-10 | 3.51e-01 | 0.0596 |
| 9842 | PLEKHM1 | LZE21T | Human | Esophagus | ESCC | 8.01e-04 | 5.69e-01 | 0.0655 |
| 9842 | PLEKHM1 | P1T-E | Human | Esophagus | ESCC | 1.43e-21 | 9.77e-01 | 0.0875 |
| 9842 | PLEKHM1 | P2T-E | Human | Esophagus | ESCC | 2.82e-03 | 1.35e-01 | 0.1177 |
| 9842 | PLEKHM1 | P4T-E | Human | Esophagus | ESCC | 1.39e-04 | 1.36e-01 | 0.1323 |
| 9842 | PLEKHM1 | P5T-E | Human | Esophagus | ESCC | 4.50e-09 | 1.72e-01 | 0.1327 |
| 9842 | PLEKHM1 | P8T-E | Human | Esophagus | ESCC | 2.07e-14 | 2.45e-01 | 0.0889 |
| 9842 | PLEKHM1 | P9T-E | Human | Esophagus | ESCC | 2.41e-09 | 2.50e-01 | 0.1131 |
| 9842 | PLEKHM1 | P10T-E | Human | Esophagus | ESCC | 6.61e-07 | 5.12e-02 | 0.116 |
| 9842 | PLEKHM1 | P11T-E | Human | Esophagus | ESCC | 1.19e-03 | 2.03e-01 | 0.1426 |
| 9842 | PLEKHM1 | P12T-E | Human | Esophagus | ESCC | 2.75e-14 | 2.53e-01 | 0.1122 |
| 9842 | PLEKHM1 | P15T-E | Human | Esophagus | ESCC | 2.28e-16 | 3.62e-01 | 0.1149 |
| 9842 | PLEKHM1 | P16T-E | Human | Esophagus | ESCC | 7.21e-06 | 7.10e-02 | 0.1153 |
| 9842 | PLEKHM1 | P17T-E | Human | Esophagus | ESCC | 5.11e-07 | 2.04e-01 | 0.1278 |
| 9842 | PLEKHM1 | P20T-E | Human | Esophagus | ESCC | 2.66e-06 | 1.50e-01 | 0.1124 |
| 9842 | PLEKHM1 | P21T-E | Human | Esophagus | ESCC | 1.03e-16 | 1.73e-01 | 0.1617 |
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| 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 |
| ∗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:001623617 | Esophagus | ESCC | macroautophagy | 216/8552 | 291/18723 | 1.94e-23 | 4.57e-21 | 216 |
| GO:001605014 | Esophagus | ESCC | vesicle organization | 211/8552 | 300/18723 | 2.85e-18 | 2.87e-16 | 211 |
| GO:000703417 | Esophagus | ESCC | vacuolar transport | 119/8552 | 157/18723 | 1.16e-14 | 6.30e-13 | 119 |
| GO:00070419 | Esophagus | ESCC | lysosomal transport | 83/8552 | 114/18723 | 3.52e-09 | 7.41e-08 | 83 |
| GO:00482844 | Esophagus | ESCC | organelle fusion | 94/8552 | 141/18723 | 3.72e-07 | 5.16e-06 | 94 |
| GO:00901743 | Esophagus | ESCC | organelle membrane fusion | 73/8552 | 110/18723 | 9.29e-06 | 8.88e-05 | 73 |
| GO:003134616 | Esophagus | ESCC | positive regulation of cell projection organization | 201/8552 | 353/18723 | 1.19e-05 | 1.11e-04 | 201 |
| GO:00069063 | Esophagus | ESCC | vesicle fusion | 70/8552 | 106/18723 | 1.82e-05 | 1.60e-04 | 70 |
| GO:00610254 | Esophagus | ESCC | membrane fusion | 98/8552 | 163/18723 | 1.39e-04 | 9.41e-04 | 98 |
| GO:00315299 | Esophagus | ESCC | ruffle organization | 39/8552 | 56/18723 | 2.44e-04 | 1.51e-03 | 39 |
| GO:00971789 | Esophagus | ESCC | ruffle assembly | 32/8552 | 44/18723 | 2.50e-04 | 1.54e-03 | 32 |
| GO:006049118 | Esophagus | ESCC | regulation of cell projection assembly | 110/8552 | 188/18723 | 2.60e-04 | 1.58e-03 | 110 |
| GO:012003218 | Esophagus | ESCC | regulation of plasma membrane bounded cell projection assembly | 108/8552 | 186/18723 | 4.37e-04 | 2.46e-03 | 108 |
| GO:01200347 | Esophagus | ESCC | positive regulation of plasma membrane bounded cell projection assembly | 64/8552 | 105/18723 | 1.15e-03 | 5.70e-03 | 64 |
| GO:19000277 | Esophagus | ESCC | regulation of ruffle assembly | 21/8552 | 31/18723 | 1.10e-02 | 3.70e-02 | 21 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa05132211 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
| hsa05132310 | Esophagus | ESCC | Salmonella infection | 191/4205 | 249/8465 | 6.51e-19 | 5.45e-17 | 2.79e-17 | 191 |
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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 |
| PLEKHM1 | SNV | Missense_Mutation | rs371593619 | c.646N>T | p.Arg216Trp | p.R216W | Q9Y4G2 | protein_coding | deleterious(0) | benign(0.241) | TCGA-A2-A04Q-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| PLEKHM1 | SNV | Missense_Mutation | novel | c.1341N>A | p.Phe447Leu | p.F447L | Q9Y4G2 | protein_coding | deleterious(0.05) | benign(0.125) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PLEKHM1 | SNV | Missense_Mutation | c.1931N>T | p.Pro644Leu | p.P644L | Q9Y4G2 | protein_coding | deleterious(0.05) | benign(0.033) | TCGA-BH-A1EO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PLEKHM1 | SNV | Missense_Mutation | c.1171N>C | p.Glu391Gln | p.E391Q | Q9Y4G2 | protein_coding | tolerated(0.55) | benign(0) | TCGA-C8-A1HM-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | CR | |
| PLEKHM1 | SNV | Missense_Mutation | c.3037N>G | p.Phe1013Val | p.F1013V | Q9Y4G2 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-D8-A1JD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| PLEKHM1 | SNV | Missense_Mutation | c.1317G>C | p.Lys439Asn | p.K439N | Q9Y4G2 | protein_coding | tolerated(0.06) | benign(0.157) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PLEKHM1 | SNV | Missense_Mutation | c.776C>T | p.Ser259Leu | p.S259L | Q9Y4G2 | protein_coding | deleterious(0.02) | probably_damaging(0.997) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| PLEKHM1 | SNV | Missense_Mutation | rs541756972 | c.356N>A | p.Arg119Gln | p.R119Q | Q9Y4G2 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-UC-A7PG-06 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | PD |
| PLEKHM1 | SNV | Missense_Mutation | c.2926N>C | p.Phe976Leu | p.F976L | Q9Y4G2 | protein_coding | deleterious(0.03) | probably_damaging(0.951) | TCGA-A6-3809-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PLEKHM1 | SNV | Missense_Mutation | rs760295037 | c.1816N>T | p.Arg606Cys | p.R606C | Q9Y4G2 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD |
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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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