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Gene: CCDC88A |
Gene summary for CCDC88A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CCDC88A | Gene ID | 55704 |
| Gene name | coiled-coil domain containing 88A | |
| Gene Alias | APE | |
| Cytomap | 2p16.1 | |
| Gene Type | protein-coding | GO ID | GO:0000226 | UniProtAcc | O14997 |
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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 |
| 55704 | CCDC88A | Pt13.b | Human | Liver | HCC | 7.13e-06 | 1.66e-01 | 0.0251 |
| 55704 | CCDC88A | Pt14.a | Human | Liver | HCC | 3.95e-04 | 3.53e-01 | 0.0169 |
| 55704 | CCDC88A | Pt14.d | Human | Liver | HCC | 2.53e-05 | 2.87e-01 | 0.0143 |
| 55704 | CCDC88A | S014 | Human | Liver | HCC | 3.22e-33 | 1.31e+00 | 0.2254 |
| 55704 | CCDC88A | S015 | Human | Liver | HCC | 1.38e-30 | 1.40e+00 | 0.2375 |
| 55704 | CCDC88A | S016 | Human | Liver | HCC | 4.27e-46 | 1.42e+00 | 0.2243 |
| 55704 | CCDC88A | S027 | Human | Liver | HCC | 3.39e-09 | 8.16e-01 | 0.2446 |
| 55704 | CCDC88A | S028 | Human | Liver | HCC | 2.95e-26 | 9.74e-01 | 0.2503 |
| 55704 | CCDC88A | S029 | Human | Liver | HCC | 3.36e-12 | 4.88e-01 | 0.2581 |
| 55704 | CCDC88A | C04 | Human | Oral cavity | OSCC | 1.01e-09 | 6.84e-01 | 0.2633 |
| 55704 | CCDC88A | C21 | Human | Oral cavity | OSCC | 4.76e-19 | 7.76e-01 | 0.2678 |
| 55704 | CCDC88A | C30 | Human | Oral cavity | OSCC | 1.54e-18 | 8.59e-01 | 0.3055 |
| 55704 | CCDC88A | C43 | Human | Oral cavity | OSCC | 3.56e-05 | 1.64e-01 | 0.1704 |
| 55704 | CCDC88A | C06 | Human | Oral cavity | OSCC | 2.72e-02 | 5.59e-01 | 0.2699 |
| 55704 | CCDC88A | EOLP-1 | Human | Oral cavity | EOLP | 1.80e-23 | 6.36e-01 | -0.0202 |
| 55704 | CCDC88A | EOLP-2 | Human | Oral cavity | EOLP | 1.69e-04 | 2.80e-01 | -0.0203 |
| 55704 | CCDC88A | NEOLP-1 | Human | Oral cavity | NEOLP | 1.07e-05 | 3.04e-01 | -0.0194 |
| 55704 | CCDC88A | NEOLP-2 | Human | Oral cavity | NEOLP | 1.81e-04 | 2.01e-01 | -0.0196 |
| 55704 | CCDC88A | SYSMH1 | Human | Oral cavity | OSCC | 7.71e-03 | 1.00e-01 | 0.1127 |
| 55704 | CCDC88A | SYSMH2 | Human | Oral cavity | OSCC | 1.74e-04 | 2.29e-01 | 0.2326 |
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:1903829111 | Esophagus | ESCC | positive regulation of cellular protein localization | 199/8552 | 276/18723 | 2.99e-19 | 3.45e-17 | 199 |
| GO:00062604 | Esophagus | ESCC | DNA replication | 181/8552 | 260/18723 | 3.55e-15 | 2.05e-13 | 181 |
| GO:0072659110 | Esophagus | ESCC | protein localization to plasma membrane | 193/8552 | 284/18723 | 1.95e-14 | 1.03e-12 | 193 |
| GO:199077819 | Esophagus | ESCC | protein localization to cell periphery | 217/8552 | 333/18723 | 4.08e-13 | 1.88e-11 | 217 |
| GO:1902905111 | Esophagus | ESCC | positive regulation of supramolecular fiber organization | 142/8552 | 209/18723 | 5.51e-11 | 1.76e-09 | 142 |
| GO:1902903111 | Esophagus | ESCC | regulation of supramolecular fiber organization | 237/8552 | 383/18723 | 9.06e-11 | 2.75e-09 | 237 |
| GO:003070518 | Esophagus | ESCC | cytoskeleton-dependent intracellular transport | 133/8552 | 195/18723 | 1.48e-10 | 4.27e-09 | 133 |
| GO:005149520 | Esophagus | ESCC | positive regulation of cytoskeleton organization | 147/8552 | 226/18723 | 2.93e-09 | 6.38e-08 | 147 |
| GO:0045185111 | Esophagus | ESCC | maintenance of protein location | 71/8552 | 94/18723 | 3.41e-09 | 7.24e-08 | 71 |
| GO:0051235110 | Esophagus | ESCC | maintenance of location | 200/8552 | 327/18723 | 1.01e-08 | 2.02e-07 | 200 |
| GO:0032507110 | Esophagus | ESCC | maintenance of protein location in cell | 52/8552 | 65/18723 | 1.41e-08 | 2.77e-07 | 52 |
| GO:000701527 | Esophagus | ESCC | actin filament organization | 259/8552 | 442/18723 | 2.37e-08 | 4.50e-07 | 259 |
| GO:0032970111 | Esophagus | ESCC | regulation of actin filament-based process | 231/8552 | 397/18723 | 2.91e-07 | 4.20e-06 | 231 |
| GO:0032956111 | Esophagus | ESCC | regulation of actin cytoskeleton organization | 210/8552 | 358/18723 | 4.40e-07 | 6.00e-06 | 210 |
| GO:003812718 | Esophagus | ESCC | ERBB signaling pathway | 82/8552 | 121/18723 | 7.23e-07 | 9.40e-06 | 82 |
| GO:011005327 | Esophagus | ESCC | regulation of actin filament organization | 166/8552 | 278/18723 | 1.54e-06 | 1.85e-05 | 166 |
| GO:00062754 | Esophagus | ESCC | regulation of DNA replication | 73/8552 | 107/18723 | 1.97e-06 | 2.28e-05 | 73 |
| GO:190211514 | Esophagus | ESCC | regulation of organelle assembly | 116/8552 | 186/18723 | 3.15e-06 | 3.53e-05 | 116 |
| GO:000717318 | Esophagus | ESCC | epidermal growth factor receptor signaling pathway | 73/8552 | 108/18723 | 3.36e-06 | 3.73e-05 | 73 |
| GO:005101727 | Esophagus | ESCC | actin filament bundle assembly | 100/8552 | 157/18723 | 3.87e-06 | 4.17e-05 | 100 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
| 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 |
| CCDC88A | SNV | Missense_Mutation | c.353C>G | p.Thr118Arg | p.T118R | Q3V6T2 | protein_coding | deleterious(0) | possibly_damaging(0.809) | TCGA-A1-A0SO-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | SD | ||
| CCDC88A | SNV | Missense_Mutation | c.1198N>G | p.Met400Val | p.M400V | Q3V6T2 | protein_coding | tolerated(0.11) | benign(0.029) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CCDC88A | SNV | Missense_Mutation | c.5200N>C | p.Val1734Leu | p.V1734L | Q3V6T2 | protein_coding | tolerated(0.35) | benign(0.001) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CCDC88A | SNV | Missense_Mutation | c.4197N>A | p.Met1399Ile | p.M1399I | Q3V6T2 | protein_coding | tolerated(0.07) | benign(0.311) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CCDC88A | SNV | Missense_Mutation | c.427N>A | p.Glu143Lys | p.E143K | Q3V6T2 | protein_coding | deleterious(0.04) | probably_damaging(0.997) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CCDC88A | SNV | Missense_Mutation | c.255N>C | p.Gln85His | p.Q85H | Q3V6T2 | protein_coding | tolerated(0.72) | benign(0.052) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CCDC88A | SNV | Missense_Mutation | novel | c.802N>A | p.Glu268Lys | p.E268K | Q3V6T2 | protein_coding | deleterious(0) | probably_damaging(0.94) | TCGA-AC-A3W5-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | CR |
| CCDC88A | SNV | Missense_Mutation | novel | c.3964N>C | p.Glu1322Gln | p.E1322Q | Q3V6T2 | protein_coding | deleterious(0.01) | probably_damaging(0.981) | TCGA-AC-A3W6-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| CCDC88A | SNV | Missense_Mutation | novel | c.5256N>G | p.Phe1752Leu | p.F1752L | Q3V6T2 | protein_coding | tolerated(0.54) | benign(0) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CCDC88A | SNV | Missense_Mutation | c.1774N>A | p.Leu592Ile | p.L592I | Q3V6T2 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 |
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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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