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Gene: CCT4 |
Gene summary for CCT4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CCT4 | Gene ID | 10575 |
| Gene name | chaperonin containing TCP1 subunit 4 | |
| Gene Alias | CCT-DELTA | |
| Cytomap | 2p15 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P50991 |
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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 |
| 10575 | CCT4 | GSM4909285 | Human | Breast | IDC | 1.23e-06 | 3.82e-01 | 0.21 |
| 10575 | CCT4 | GSM4909286 | Human | Breast | IDC | 6.21e-05 | -2.90e-01 | 0.1081 |
| 10575 | CCT4 | GSM4909294 | Human | Breast | IDC | 1.28e-05 | -2.48e-01 | 0.2022 |
| 10575 | CCT4 | GSM4909296 | Human | Breast | IDC | 3.73e-20 | -4.32e-01 | 0.1524 |
| 10575 | CCT4 | GSM4909297 | Human | Breast | IDC | 4.01e-17 | -2.80e-01 | 0.1517 |
| 10575 | CCT4 | GSM4909298 | Human | Breast | IDC | 5.16e-05 | -2.45e-01 | 0.1551 |
| 10575 | CCT4 | GSM4909301 | Human | Breast | IDC | 7.16e-09 | -3.30e-01 | 0.1577 |
| 10575 | CCT4 | GSM4909302 | Human | Breast | IDC | 1.26e-08 | -4.19e-01 | 0.1545 |
| 10575 | CCT4 | GSM4909307 | Human | Breast | IDC | 2.51e-07 | -3.41e-01 | 0.1569 |
| 10575 | CCT4 | GSM4909309 | Human | Breast | IDC | 3.82e-12 | -4.46e-01 | 0.0483 |
| 10575 | CCT4 | GSM4909311 | Human | Breast | IDC | 1.72e-42 | -4.65e-01 | 0.1534 |
| 10575 | CCT4 | GSM4909312 | Human | Breast | IDC | 3.04e-18 | -1.80e-01 | 0.1552 |
| 10575 | CCT4 | GSM4909313 | Human | Breast | IDC | 1.25e-02 | -2.74e-01 | 0.0391 |
| 10575 | CCT4 | GSM4909319 | Human | Breast | IDC | 7.00e-47 | -5.75e-01 | 0.1563 |
| 10575 | CCT4 | GSM4909320 | Human | Breast | IDC | 3.00e-03 | -3.57e-01 | 0.1575 |
| 10575 | CCT4 | GSM4909321 | Human | Breast | IDC | 5.42e-20 | -2.87e-01 | 0.1559 |
| 10575 | CCT4 | brca1 | Human | Breast | Precancer | 8.78e-05 | 2.84e-01 | -0.0338 |
| 10575 | CCT4 | NCCBC14 | Human | Breast | DCIS | 4.50e-07 | -1.42e-01 | 0.2021 |
| 10575 | CCT4 | NCCBC2 | Human | Breast | DCIS | 8.42e-04 | -5.43e-01 | 0.1554 |
| 10575 | CCT4 | NCCBC3 | Human | Breast | DCIS | 1.18e-02 | -1.32e-01 | 0.1198 |
| 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:007020313 | Endometrium | EEC | regulation of establishment of protein localization to telomere | 8/2168 | 11/18723 | 3.81e-06 | 1.01e-04 | 8 |
| GO:190486913 | Endometrium | EEC | regulation of protein localization to Cajal body | 8/2168 | 11/18723 | 3.81e-06 | 1.01e-04 | 8 |
| GO:190487113 | Endometrium | EEC | positive regulation of protein localization to Cajal body | 8/2168 | 11/18723 | 3.81e-06 | 1.01e-04 | 8 |
| GO:199017313 | Endometrium | EEC | protein localization to nucleoplasm | 9/2168 | 14/18723 | 4.27e-06 | 1.10e-04 | 9 |
| GO:003450413 | Endometrium | EEC | protein localization to nucleus | 60/2168 | 290/18723 | 5.09e-06 | 1.26e-04 | 60 |
| GO:000700414 | Endometrium | EEC | telomere maintenance via telomerase | 22/2168 | 69/18723 | 5.88e-06 | 1.42e-04 | 22 |
| GO:200027814 | Endometrium | EEC | regulation of DNA biosynthetic process | 29/2168 | 106/18723 | 6.68e-06 | 1.58e-04 | 29 |
| GO:190340513 | Endometrium | EEC | protein localization to nuclear body | 8/2168 | 12/18723 | 1.03e-05 | 2.22e-04 | 8 |
| GO:190481613 | Endometrium | EEC | positive regulation of protein localization to chromosome, telomeric region | 8/2168 | 12/18723 | 1.03e-05 | 2.22e-04 | 8 |
| GO:190486713 | Endometrium | EEC | protein localization to Cajal body | 8/2168 | 12/18723 | 1.03e-05 | 2.22e-04 | 8 |
| GO:190018213 | Endometrium | EEC | positive regulation of protein localization to nucleus | 25/2168 | 87/18723 | 1.12e-05 | 2.34e-04 | 25 |
| GO:000627813 | Endometrium | EEC | RNA-dependent DNA biosynthetic process | 22/2168 | 75/18723 | 2.59e-05 | 4.56e-04 | 22 |
| GO:001083314 | Endometrium | EEC | telomere maintenance via telomere lengthening | 23/2168 | 81/18723 | 3.05e-05 | 5.29e-04 | 23 |
| GO:190435814 | Endometrium | EEC | positive regulation of telomere maintenance via telomere lengthening | 14/2168 | 37/18723 | 3.41e-05 | 5.78e-04 | 14 |
| GO:003220613 | Endometrium | EEC | positive regulation of telomere maintenance | 17/2168 | 52/18723 | 4.62e-05 | 7.45e-04 | 17 |
| GO:190481412 | Endometrium | EEC | regulation of protein localization to chromosome, telomeric region | 8/2168 | 14/18723 | 5.02e-05 | 8.06e-04 | 8 |
| GO:003221213 | Endometrium | EEC | positive regulation of telomere maintenance via telomerase | 13/2168 | 34/18723 | 5.71e-05 | 8.96e-04 | 13 |
| GO:003221013 | Endometrium | EEC | regulation of telomere maintenance via telomerase | 17/2168 | 53/18723 | 6.07e-05 | 9.21e-04 | 17 |
| GO:190018013 | Endometrium | EEC | regulation of protein localization to nucleus | 32/2168 | 136/18723 | 6.37e-05 | 9.48e-04 | 32 |
| GO:007189713 | Endometrium | EEC | DNA biosynthetic process | 39/2168 | 180/18723 | 7.68e-05 | 1.11e-03 | 39 |
| 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 47 |
| 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 |
| CCT4 | SNV | Missense_Mutation | rs780164717 | c.1487N>A | p.Arg496Gln | p.R496Q | P50991 | protein_coding | tolerated(0.09) | probably_damaging(0.924) | TCGA-D8-A1J9-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CCT4 | SNV | Missense_Mutation | novel | c.898A>T | p.Ile300Leu | p.I300L | P50991 | protein_coding | tolerated(0.07) | benign(0.034) | TCGA-E2-A576-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD |
| CCT4 | insertion | In_Frame_Ins | novel | c.1072_1073insTAGAGAAAAGCTCATCACCCAGGC | p.Ser358delinsLeuGluLysSerSerSerProArgPro | p.S358delinsLEKSSSPRP | P50991 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
| CCT4 | SNV | Missense_Mutation | novel | c.595A>G | p.Thr199Ala | p.T199A | P50991 | protein_coding | tolerated(0.32) | benign(0.021) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| CCT4 | SNV | Missense_Mutation | novel | c.1223C>T | p.Ala408Val | p.A408V | P50991 | protein_coding | deleterious(0.04) | probably_damaging(1) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CCT4 | SNV | Missense_Mutation | rs140356041 | c.967N>G | p.Met323Val | p.M323V | P50991 | protein_coding | deleterious(0.01) | benign(0.338) | TCGA-AA-A02R-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| CCT4 | SNV | Missense_Mutation | c.881N>A | p.Gly294Glu | p.G294E | P50991 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CM-5341-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | fluorouracil | SD | |
| CCT4 | SNV | Missense_Mutation | rs769218948 | c.1159N>G | p.Thr387Ala | p.T387A | P50991 | protein_coding | deleterious(0.01) | benign(0.071) | TCGA-AG-4001-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CCT4 | SNV | Missense_Mutation | c.1512G>T | p.Leu504Phe | p.L504F | P50991 | protein_coding | tolerated(0.17) | benign(0.025) | TCGA-AG-4022-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| CCT4 | insertion | Nonsense_Mutation | novel | c.1386_1387insAATTAATCAATATTT | p.Pro462_Ser463insAsnTerSerIlePhe | p.P462_S463insN*SIF | P50991 | protein_coding | TCGA-AM-5820-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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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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