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Gene: CLPTM1 |
Gene summary for CLPTM1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CLPTM1 | Gene ID | 1209 |
| Gene name | CLPTM1 regulator of GABA type A receptor forward trafficking | |
| Gene Alias | CLPTM1 | |
| Cytomap | 19q13.32 | |
| Gene Type | protein-coding | GO ID | GO:0001775 | UniProtAcc | O96005 |
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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 |
| 1209 | CLPTM1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.81e-02 | 1.72e-01 | 0.0155 |
| 1209 | CLPTM1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 6.88e-08 | 5.07e-01 | -0.1808 |
| 1209 | CLPTM1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 5.90e-03 | 4.20e-01 | -0.0811 |
| 1209 | CLPTM1 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.56e-08 | 4.60e-01 | -0.1954 |
| 1209 | CLPTM1 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.20e-03 | 4.58e-01 | -0.1526 |
| 1209 | CLPTM1 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.11e-16 | 5.90e-01 | -0.1464 |
| 1209 | CLPTM1 | HTA11_866_2000001011 | Human | Colorectum | AD | 9.76e-06 | 2.97e-01 | -0.1001 |
| 1209 | CLPTM1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.26e-13 | 6.30e-01 | -0.059 |
| 1209 | CLPTM1 | HTA11_546_2000001011 | Human | Colorectum | AD | 8.48e-04 | 5.48e-01 | -0.0842 |
| 1209 | CLPTM1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 2.85e-02 | 3.44e-01 | 0.0338 |
| 1209 | CLPTM1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 7.13e-24 | 6.59e-01 | 0.0674 |
| 1209 | CLPTM1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.26e-08 | 3.92e-01 | 0.3859 |
| 1209 | CLPTM1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 3.61e-02 | 2.75e-01 | 0.3005 |
| 1209 | CLPTM1 | A002-C-201 | Human | Colorectum | FAP | 3.68e-02 | -1.31e-01 | 0.0324 |
| 1209 | CLPTM1 | A002-C-116 | Human | Colorectum | FAP | 9.36e-06 | -1.24e-01 | -0.0452 |
| 1209 | CLPTM1 | LZE2T | Human | Esophagus | ESCC | 3.39e-04 | 9.01e-01 | 0.082 |
| 1209 | CLPTM1 | LZE4T | Human | Esophagus | ESCC | 5.05e-06 | 3.25e-01 | 0.0811 |
| 1209 | CLPTM1 | LZE5T | Human | Esophagus | ESCC | 1.66e-05 | 4.06e-01 | 0.0514 |
| 1209 | CLPTM1 | LZE7T | Human | Esophagus | ESCC | 2.89e-03 | 3.73e-01 | 0.0667 |
| 1209 | CLPTM1 | LZE8T | Human | Esophagus | ESCC | 7.60e-07 | 6.78e-02 | 0.067 |
| Page: 1 2 3 4 5 6 7 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:1903706 | Colorectum | AD | regulation of hemopoiesis | 99/3918 | 367/18723 | 3.08e-03 | 2.28e-02 | 99 |
| GO:19037061 | Colorectum | MSS | regulation of hemopoiesis | 89/3467 | 367/18723 | 3.39e-03 | 2.56e-02 | 89 |
| GO:1903131 | Colorectum | FAP | mononuclear cell differentiation | 79/2622 | 426/18723 | 5.00e-03 | 3.33e-02 | 79 |
| GO:19037063 | Colorectum | FAP | regulation of hemopoiesis | 69/2622 | 367/18723 | 6.01e-03 | 3.78e-02 | 69 |
| GO:190370620 | Esophagus | HGIN | regulation of hemopoiesis | 69/2587 | 367/18723 | 4.39e-03 | 3.86e-02 | 69 |
| GO:1903706110 | Esophagus | ESCC | regulation of hemopoiesis | 201/8552 | 367/18723 | 2.60e-04 | 1.58e-03 | 201 |
| GO:004211018 | Esophagus | ESCC | T cell activation | 256/8552 | 487/18723 | 1.18e-03 | 5.87e-03 | 256 |
| GO:19031317 | Esophagus | ESCC | mononuclear cell differentiation | 226/8552 | 426/18723 | 1.20e-03 | 5.88e-03 | 226 |
| GO:190210510 | Esophagus | ESCC | regulation of leukocyte differentiation | 152/8552 | 279/18723 | 1.82e-03 | 8.35e-03 | 152 |
| GO:00302176 | Esophagus | ESCC | T cell differentiation | 137/8552 | 257/18723 | 8.09e-03 | 2.87e-02 | 137 |
| GO:00300984 | Esophagus | ESCC | lymphocyte differentiation | 192/8552 | 374/18723 | 1.52e-02 | 4.93e-02 | 192 |
| GO:004211016 | Oral cavity | OSCC | T cell activation | 245/7305 | 487/18723 | 2.00e-07 | 3.22e-06 | 245 |
| GO:19031316 | Oral cavity | OSCC | mononuclear cell differentiation | 210/7305 | 426/18723 | 8.44e-06 | 9.02e-05 | 210 |
| GO:190370618 | Oral cavity | OSCC | regulation of hemopoiesis | 180/7305 | 367/18723 | 5.16e-05 | 4.30e-04 | 180 |
| GO:005086315 | Oral cavity | OSCC | regulation of T cell activation | 161/7305 | 329/18723 | 1.44e-04 | 1.02e-03 | 161 |
| GO:00300983 | Oral cavity | OSCC | lymphocyte differentiation | 179/7305 | 374/18723 | 2.74e-04 | 1.74e-03 | 179 |
| GO:19021059 | Oral cavity | OSCC | regulation of leukocyte differentiation | 136/7305 | 279/18723 | 5.53e-04 | 3.21e-03 | 136 |
| GO:00302175 | Oral cavity | OSCC | T cell differentiation | 126/7305 | 257/18723 | 6.51e-04 | 3.66e-03 | 126 |
| GO:00330771 | Oral cavity | OSCC | T cell differentiation in thymus | 42/7305 | 75/18723 | 2.09e-03 | 9.63e-03 | 42 |
| GO:00456194 | Oral cavity | OSCC | regulation of lymphocyte differentiation | 83/7305 | 174/18723 | 1.18e-02 | 4.00e-02 | 83 |
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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 |
| 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 |
| CLPTM1 | SNV | Missense_Mutation | c.921N>G | p.Phe307Leu | p.F307L | O96005 | protein_coding | tolerated(0.05) | benign(0.026) | TCGA-A8-A097-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| CLPTM1 | SNV | Missense_Mutation | rs199925354 | c.886N>A | p.Glu296Lys | p.E296K | O96005 | protein_coding | tolerated(0.08) | benign(0.148) | TCGA-C8-A274-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
| CLPTM1 | insertion | Nonsense_Mutation | novel | c.182_183insAGGACAGCAAAAGACTCTCTAGGTCACCACTGTCCC | p.Phe61delinsLeuGlyGlnGlnLysThrLeuTerValThrThrValPro | p.F61delinsLGQQKTL*VTTVP | O96005 | protein_coding | TCGA-BH-A0B3-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | ||
| CLPTM1 | deletion | Frame_Shift_Del | novel | c.829delN | p.Ile278SerfsTer68 | p.I278Sfs*68 | O96005 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
| CLPTM1 | SNV | Missense_Mutation | novel | c.152N>C | p.Asn51Thr | p.N51T | O96005 | protein_coding | deleterious(0.02) | probably_damaging(0.982) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CLPTM1 | SNV | Missense_Mutation | novel | c.1579N>T | p.Leu527Phe | p.L527F | O96005 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CLPTM1 | SNV | Missense_Mutation | novel | c.114N>C | p.Glu38Asp | p.E38D | O96005 | protein_coding | tolerated(0.16) | benign(0.003) | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
| CLPTM1 | SNV | Missense_Mutation | novel | c.1137C>G | p.Ile379Met | p.I379M | O96005 | protein_coding | deleterious(0.01) | probably_damaging(0.932) | TCGA-MA-AA41-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| CLPTM1 | SNV | Missense_Mutation | c.656N>G | p.Asp219Gly | p.D219G | O96005 | protein_coding | tolerated(0.17) | benign(0.03) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CLPTM1 | SNV | Missense_Mutation | rs770360744 | c.1198N>A | p.Val400Ile | p.V400I | O96005 | protein_coding | tolerated(0.2) | possibly_damaging(0.457) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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