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Gene: CCDC28A |
Gene summary for CCDC28A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CCDC28A | Gene ID | 25901 |
| Gene name | coiled-coil domain containing 28A | |
| Gene Alias | C6orf80 | |
| Cytomap | 6q24.1 | |
| Gene Type | protein-coding | GO ID | GO:0003674 | UniProtAcc | Q8IWP9 |
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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 |
| 25901 | CCDC28A | LZE4T | Human | Esophagus | ESCC | 7.37e-19 | 2.79e-01 | 0.0811 |
| 25901 | CCDC28A | LZE8T | Human | Esophagus | ESCC | 9.02e-08 | 1.66e-01 | 0.067 |
| 25901 | CCDC28A | LZE22D1 | Human | Esophagus | HGIN | 8.09e-03 | 7.17e-02 | 0.0595 |
| 25901 | CCDC28A | LZE22T | Human | Esophagus | ESCC | 1.40e-03 | 1.98e-01 | 0.068 |
| 25901 | CCDC28A | LZE24T | Human | Esophagus | ESCC | 3.26e-20 | 5.84e-01 | 0.0596 |
| 25901 | CCDC28A | LZE6T | Human | Esophagus | ESCC | 3.50e-06 | 1.10e-01 | 0.0845 |
| 25901 | CCDC28A | P1T-E | Human | Esophagus | ESCC | 2.09e-05 | 3.85e-01 | 0.0875 |
| 25901 | CCDC28A | P2T-E | Human | Esophagus | ESCC | 2.49e-21 | 2.98e-01 | 0.1177 |
| 25901 | CCDC28A | P4T-E | Human | Esophagus | ESCC | 6.40e-18 | 2.82e-01 | 0.1323 |
| 25901 | CCDC28A | P5T-E | Human | Esophagus | ESCC | 1.53e-16 | 1.81e-01 | 0.1327 |
| 25901 | CCDC28A | P8T-E | Human | Esophagus | ESCC | 2.29e-21 | 3.81e-01 | 0.0889 |
| 25901 | CCDC28A | P9T-E | Human | Esophagus | ESCC | 1.84e-10 | 1.68e-01 | 0.1131 |
| 25901 | CCDC28A | P10T-E | Human | Esophagus | ESCC | 3.27e-21 | 3.23e-01 | 0.116 |
| 25901 | CCDC28A | P11T-E | Human | Esophagus | ESCC | 3.11e-04 | 2.39e-01 | 0.1426 |
| 25901 | CCDC28A | P12T-E | Human | Esophagus | ESCC | 2.05e-17 | 3.33e-01 | 0.1122 |
| 25901 | CCDC28A | P15T-E | Human | Esophagus | ESCC | 8.44e-19 | 5.44e-01 | 0.1149 |
| 25901 | CCDC28A | P16T-E | Human | Esophagus | ESCC | 8.85e-32 | 6.06e-01 | 0.1153 |
| 25901 | CCDC28A | P17T-E | Human | Esophagus | ESCC | 7.23e-03 | 8.02e-02 | 0.1278 |
| 25901 | CCDC28A | P19T-E | Human | Esophagus | ESCC | 4.72e-03 | 4.62e-01 | 0.1662 |
| 25901 | CCDC28A | P20T-E | Human | Esophagus | ESCC | 1.55e-13 | 2.15e-01 | 0.1124 |
| Page: 1 2 3 4 5 6 |
| 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 | ||
| 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 | ||
| 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 |
| Page: 1 |
| 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 |
| CCDC28A | SNV | Missense_Mutation | novel | c.308N>G | p.Ser103Cys | p.S103C | Q8IWP9 | protein_coding | deleterious(0.01) | probably_damaging(0.981) | TCGA-GM-A2DA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | fluorouracil | PD |
| CCDC28A | insertion | In_Frame_Ins | novel | c.178_179insAAAATCATGGCAATAGTCTCATATCTATATTAGATGAAGTCATGC | p.Val60delinsGluAsnHisGlyAsnSerLeuIleSerIleLeuAspGluValMetLeu | p.V60delinsENHGNSLISILDEVML | Q8IWP9 | protein_coding | TCGA-AR-A0TP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| CCDC28A | deletion | Frame_Shift_Del | rs750567585 | c.309delN | p.Phe104LeufsTer18 | p.F104Lfs*18 | Q8IWP9 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| CCDC28A | SNV | Missense_Mutation | novel | c.205G>A | p.Gly69Ser | p.G69S | Q8IWP9 | protein_coding | tolerated_low_confidence(0.14) | benign(0.018) | TCGA-EA-A5ZE-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
| CCDC28A | SNV | Missense_Mutation | c.562N>T | p.Asp188Tyr | p.D188Y | Q8IWP9 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| CCDC28A | SNV | Missense_Mutation | c.112N>T | p.Arg38Trp | p.R38W | Q8IWP9 | protein_coding | tolerated_low_confidence(0.1) | benign(0) | TCGA-AZ-6599-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| CCDC28A | SNV | Missense_Mutation | c.642N>T | p.Glu214Asp | p.E214D | Q8IWP9 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
| CCDC28A | SNV | Missense_Mutation | rs369021139 | c.413G>A | p.Arg138Gln | p.R138Q | Q8IWP9 | protein_coding | deleterious(0) | possibly_damaging(0.688) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| CCDC28A | SNV | Missense_Mutation | novel | c.787N>A | p.Ala263Thr | p.A263T | Q8IWP9 | protein_coding | deleterious(0.04) | probably_damaging(0.996) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CCDC28A | SNV | Missense_Mutation | c.806C>A | p.Pro269Gln | p.P269Q | Q8IWP9 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.998) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | 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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