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Gene: TCP1 |
Gene summary for TCP1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | TCP1 | Gene ID | 6950 |
| Gene name | t-complex 1 | |
| Gene Alias | CCT-alpha | |
| Cytomap | 6q25.3 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | E7EQR6 |
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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 |
| 6950 | TCP1 | GSM4909277 | Human | Breast | Precancer | 4.84e-06 | 5.52e-01 | 0.0177 |
| 6950 | TCP1 | GSM4909285 | Human | Breast | IDC | 7.02e-09 | 3.16e-01 | 0.21 |
| 6950 | TCP1 | GSM4909286 | Human | Breast | IDC | 1.72e-03 | 9.92e-03 | 0.1081 |
| 6950 | TCP1 | GSM4909293 | Human | Breast | IDC | 2.28e-02 | -1.72e-01 | 0.1581 |
| 6950 | TCP1 | GSM4909296 | Human | Breast | IDC | 3.13e-19 | -5.37e-01 | 0.1524 |
| 6950 | TCP1 | GSM4909297 | Human | Breast | IDC | 1.43e-17 | -4.55e-01 | 0.1517 |
| 6950 | TCP1 | GSM4909298 | Human | Breast | IDC | 6.92e-05 | -2.70e-01 | 0.1551 |
| 6950 | TCP1 | GSM4909301 | Human | Breast | IDC | 6.07e-11 | -4.10e-01 | 0.1577 |
| 6950 | TCP1 | GSM4909302 | Human | Breast | IDC | 3.62e-15 | -5.13e-01 | 0.1545 |
| 6950 | TCP1 | GSM4909304 | Human | Breast | IDC | 4.33e-05 | -3.20e-01 | 0.1636 |
| 6950 | TCP1 | GSM4909307 | Human | Breast | IDC | 4.02e-09 | -4.13e-01 | 0.1569 |
| 6950 | TCP1 | GSM4909309 | Human | Breast | IDC | 3.59e-12 | -5.17e-01 | 0.0483 |
| 6950 | TCP1 | GSM4909311 | Human | Breast | IDC | 3.18e-34 | -5.70e-01 | 0.1534 |
| 6950 | TCP1 | GSM4909312 | Human | Breast | IDC | 3.93e-09 | -2.61e-01 | 0.1552 |
| 6950 | TCP1 | GSM4909313 | Human | Breast | IDC | 2.15e-04 | -3.56e-01 | 0.0391 |
| 6950 | TCP1 | GSM4909315 | Human | Breast | IDC | 5.62e-05 | -3.45e-01 | 0.21 |
| 6950 | TCP1 | GSM4909319 | Human | Breast | IDC | 8.32e-37 | -6.19e-01 | 0.1563 |
| 6950 | TCP1 | GSM4909320 | Human | Breast | IDC | 2.06e-10 | -5.51e-01 | 0.1575 |
| 6950 | TCP1 | GSM4909321 | Human | Breast | IDC | 1.92e-14 | -3.25e-01 | 0.1559 |
| 6950 | TCP1 | brca1 | Human | Breast | Precancer | 5.45e-03 | 3.08e-01 | -0.0338 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:005105213 | Oral cavity | LP | regulation of DNA metabolic process | 125/4623 | 359/18723 | 9.43e-06 | 1.75e-04 | 125 |
| GO:009067014 | Oral cavity | LP | RNA localization to Cajal body | 14/4623 | 19/18723 | 9.75e-06 | 1.78e-04 | 14 |
| GO:009067114 | Oral cavity | LP | telomerase RNA localization to Cajal body | 14/4623 | 19/18723 | 9.75e-06 | 1.78e-04 | 14 |
| GO:009067214 | Oral cavity | LP | telomerase RNA localization | 14/4623 | 19/18723 | 9.75e-06 | 1.78e-04 | 14 |
| GO:009068514 | Oral cavity | LP | RNA localization to nucleus | 14/4623 | 19/18723 | 9.75e-06 | 1.78e-04 | 14 |
| GO:005105415 | Oral cavity | LP | positive regulation of DNA metabolic process | 77/4623 | 201/18723 | 1.20e-05 | 2.15e-04 | 77 |
| GO:190485116 | Oral cavity | LP | positive regulation of establishment of protein localization to telomere | 9/4623 | 10/18723 | 2.64e-05 | 4.21e-04 | 9 |
| GO:007020216 | Oral cavity | LP | regulation of establishment of protein localization to chromosome | 10/4623 | 12/18723 | 3.32e-05 | 5.02e-04 | 10 |
| GO:190481615 | Oral cavity | LP | positive regulation of protein localization to chromosome, telomeric region | 10/4623 | 12/18723 | 3.32e-05 | 5.02e-04 | 10 |
| GO:190481414 | Oral cavity | LP | regulation of protein localization to chromosome, telomeric region | 11/4623 | 14/18723 | 3.49e-05 | 5.22e-04 | 11 |
| GO:200027818 | Oral cavity | LP | regulation of DNA biosynthetic process | 45/4623 | 106/18723 | 4.42e-05 | 6.30e-04 | 45 |
| GO:003220415 | Oral cavity | LP | regulation of telomere maintenance | 36/4623 | 80/18723 | 5.80e-05 | 7.94e-04 | 36 |
| GO:003304415 | Oral cavity | LP | regulation of chromosome organization | 70/4623 | 187/18723 | 6.89e-05 | 9.22e-04 | 70 |
| GO:000700416 | Oral cavity | LP | telomere maintenance via telomerase | 32/4623 | 69/18723 | 7.20e-05 | 9.49e-04 | 32 |
| GO:001083317 | Oral cavity | LP | telomere maintenance via telomere lengthening | 36/4623 | 81/18723 | 7.97e-05 | 1.03e-03 | 36 |
| GO:200125217 | Oral cavity | LP | positive regulation of chromosome organization | 36/4623 | 82/18723 | 1.09e-04 | 1.31e-03 | 36 |
| GO:007020014 | Oral cavity | LP | establishment of protein localization to telomere | 11/4623 | 16/18723 | 2.52e-04 | 2.63e-03 | 11 |
| GO:003220013 | Oral cavity | LP | telomere organization | 59/4623 | 159/18723 | 3.21e-04 | 3.25e-03 | 59 |
| GO:007019814 | Oral cavity | LP | protein localization to chromosome, telomeric region | 16/4623 | 29/18723 | 4.23e-04 | 4.08e-03 | 16 |
| GO:000627815 | Oral cavity | LP | RNA-dependent DNA biosynthetic process | 32/4623 | 75/18723 | 4.78e-04 | 4.49e-03 | 32 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 |
| 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 |
| TCP1 | SNV | Missense_Mutation | novel | c.1640N>G | p.Asp547Gly | p.D547G | P17987 | protein_coding | tolerated_low_confidence(0.12) | benign(0.007) | TCGA-A7-A6VW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| TCP1 | deletion | Frame_Shift_Del | c.1430delN | p.Asn477ThrfsTer7 | p.N477Tfs*7 | P17987 | protein_coding | TCGA-E9-A1RF-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD | |||
| TCP1 | SNV | Missense_Mutation | novel | c.1555N>C | p.Glu519Gln | p.E519Q | P17987 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C5-A1MH-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | PD |
| TCP1 | SNV | Missense_Mutation | novel | c.396N>G | p.Ile132Met | p.I132M | P17987 | protein_coding | tolerated(0.2) | possibly_damaging(0.706) | TCGA-VS-A8EL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| TCP1 | SNV | Missense_Mutation | c.1438N>T | p.Arg480Cys | p.R480C | P17987 | protein_coding | deleterious(0.02) | possibly_damaging(0.579) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD | |
| TCP1 | SNV | Missense_Mutation | c.10N>T | p.Pro4Ser | p.P4S | P17987 | protein_coding | tolerated_low_confidence(0.17) | benign(0) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
| TCP1 | SNV | Missense_Mutation | novel | c.501N>A | p.Phe167Leu | p.F167L | P17987 | protein_coding | tolerated(0.26) | benign(0.044) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| TCP1 | SNV | Missense_Mutation | rs760874138 | c.1297N>T | p.Arg433Trp | p.R433W | P17987 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-CA-5255-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| TCP1 | SNV | Missense_Mutation | c.1064N>T | p.Arg355Ile | p.R355I | P17987 | protein_coding | deleterious(0.03) | possibly_damaging(0.781) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR | |
| TCP1 | SNV | Missense_Mutation | novel | c.944N>G | p.Asp315Gly | p.D315G | P17987 | protein_coding | deleterious(0) | probably_damaging(0.929) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| 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 |
| Page: 1 |
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