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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 |
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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:007019811 | Liver | HCC | protein localization to chromosome, telomeric region | 22/7958 | 29/18723 | 2.73e-04 | 1.98e-03 | 22 |
GO:00718975 | Liver | HCC | DNA biosynthetic process | 99/7958 | 180/18723 | 4.66e-04 | 3.08e-03 | 99 |
GO:19048721 | Liver | HCC | regulation of telomerase RNA localization to Cajal body | 15/7958 | 18/18723 | 4.74e-04 | 3.12e-03 | 15 |
GO:19048741 | Liver | HCC | positive regulation of telomerase RNA localization to Cajal body | 13/7958 | 15/18723 | 5.67e-04 | 3.61e-03 | 13 |
GO:190435812 | Liver | HCC | positive regulation of telomere maintenance via telomere lengthening | 26/7958 | 37/18723 | 5.88e-04 | 3.74e-03 | 26 |
GO:007020212 | Liver | HCC | regulation of establishment of protein localization to chromosome | 11/7958 | 12/18723 | 5.97e-04 | 3.75e-03 | 11 |
GO:190340511 | Liver | HCC | protein localization to nuclear body | 11/7958 | 12/18723 | 5.97e-04 | 3.75e-03 | 11 |
GO:190481611 | Liver | HCC | positive regulation of protein localization to chromosome, telomeric region | 11/7958 | 12/18723 | 5.97e-04 | 3.75e-03 | 11 |
GO:190486711 | Liver | HCC | protein localization to Cajal body | 11/7958 | 12/18723 | 5.97e-04 | 3.75e-03 | 11 |
GO:00345021 | Liver | HCC | protein localization to chromosome | 55/7958 | 92/18723 | 6.12e-04 | 3.82e-03 | 55 |
GO:003221211 | Liver | HCC | positive regulation of telomere maintenance via telomerase | 24/7958 | 34/18723 | 8.62e-04 | 5.13e-03 | 24 |
GO:200057312 | Liver | HCC | positive regulation of DNA biosynthetic process | 41/7958 | 66/18723 | 1.02e-03 | 5.86e-03 | 41 |
GO:19048141 | Liver | HCC | regulation of protein localization to chromosome, telomeric region | 12/7958 | 14/18723 | 1.17e-03 | 6.54e-03 | 12 |
GO:007020311 | Liver | HCC | regulation of establishment of protein localization to telomere | 10/7958 | 11/18723 | 1.30e-03 | 7.01e-03 | 10 |
GO:00906701 | Liver | HCC | RNA localization to Cajal body | 15/7958 | 19/18723 | 1.36e-03 | 7.28e-03 | 15 |
GO:00906711 | Liver | HCC | telomerase RNA localization to Cajal body | 15/7958 | 19/18723 | 1.36e-03 | 7.28e-03 | 15 |
GO:00906721 | Liver | HCC | telomerase RNA localization | 15/7958 | 19/18723 | 1.36e-03 | 7.28e-03 | 15 |
GO:00906851 | Liver | HCC | RNA localization to nucleus | 15/7958 | 19/18723 | 1.36e-03 | 7.28e-03 | 15 |
GO:00322001 | Liver | HCC | telomere organization | 86/7958 | 159/18723 | 2.06e-03 | 1.04e-02 | 86 |
GO:190485112 | Liver | HCC | positive regulation of establishment of protein localization to telomere | 9/7958 | 10/18723 | 2.79e-03 | 1.31e-02 | 9 |
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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 |
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 |
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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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