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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 | LZE4T | Human | Esophagus | ESCC | 1.25e-06 | 3.19e-01 | 0.0811 |
55704 | CCDC88A | LZE22T | Human | Esophagus | ESCC | 1.16e-02 | 2.19e-01 | 0.068 |
55704 | CCDC88A | LZE24T | Human | Esophagus | ESCC | 2.93e-05 | 1.78e-01 | 0.0596 |
55704 | CCDC88A | P2T-E | Human | Esophagus | ESCC | 5.62e-61 | 1.16e+00 | 0.1177 |
55704 | CCDC88A | P4T-E | Human | Esophagus | ESCC | 7.50e-27 | 6.16e-01 | 0.1323 |
55704 | CCDC88A | P5T-E | Human | Esophagus | ESCC | 3.29e-11 | 3.29e-01 | 0.1327 |
55704 | CCDC88A | P8T-E | Human | Esophagus | ESCC | 3.41e-06 | 1.01e-01 | 0.0889 |
55704 | CCDC88A | P9T-E | Human | Esophagus | ESCC | 9.61e-07 | 2.04e-01 | 0.1131 |
55704 | CCDC88A | P10T-E | Human | Esophagus | ESCC | 4.74e-18 | 3.72e-01 | 0.116 |
55704 | CCDC88A | P11T-E | Human | Esophagus | ESCC | 1.58e-09 | 3.54e-01 | 0.1426 |
55704 | CCDC88A | P12T-E | Human | Esophagus | ESCC | 1.33e-20 | 5.22e-01 | 0.1122 |
55704 | CCDC88A | P15T-E | Human | Esophagus | ESCC | 4.46e-18 | 5.72e-01 | 0.1149 |
55704 | CCDC88A | P16T-E | Human | Esophagus | ESCC | 1.55e-18 | 4.15e-01 | 0.1153 |
55704 | CCDC88A | P17T-E | Human | Esophagus | ESCC | 2.93e-03 | 2.53e-01 | 0.1278 |
55704 | CCDC88A | P19T-E | Human | Esophagus | ESCC | 1.70e-03 | 4.84e-01 | 0.1662 |
55704 | CCDC88A | P20T-E | Human | Esophagus | ESCC | 8.36e-13 | 3.71e-01 | 0.1124 |
55704 | CCDC88A | P21T-E | Human | Esophagus | ESCC | 1.69e-20 | 5.56e-01 | 0.1617 |
55704 | CCDC88A | P22T-E | Human | Esophagus | ESCC | 3.62e-07 | 3.69e-02 | 0.1236 |
55704 | CCDC88A | P23T-E | Human | Esophagus | ESCC | 6.12e-07 | 2.69e-01 | 0.108 |
55704 | CCDC88A | P24T-E | Human | Esophagus | ESCC | 3.86e-09 | 1.96e-01 | 0.1287 |
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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: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 |
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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 |
CCDC88A | deletion | Frame_Shift_Del | c.2032delA | p.Thr678HisfsTer8 | p.T678Hfs*8 | Q3V6T2 | protein_coding | TCGA-BR-8487-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |||
CCDC88A | insertion | In_Frame_Ins | novel | c.3963_3964insATATTTGTT | p.Glu1321_Glu1322insIlePheVal | p.E1321_E1322insIFV | Q3V6T2 | protein_coding | TCGA-BR-8677-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
CCDC88A | insertion | Frame_Shift_Ins | rs750732366 | c.2032_2033insA | p.Thr678AsnfsTer4 | p.T678Nfs*4 | Q3V6T2 | protein_coding | TCGA-CG-4306-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | ||
CCDC88A | insertion | Frame_Shift_Ins | rs750732366 | c.2032dupA | p.Thr678AsnfsTer4 | p.T678Nfs*4 | Q3V6T2 | protein_coding | TCGA-CG-4442-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
CCDC88A | deletion | Frame_Shift_Del | novel | c.1845delA | p.Glu616AsnfsTer33 | p.E616Nfs*33 | Q3V6T2 | protein_coding | TCGA-F1-6874-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
CCDC88A | deletion | Frame_Shift_Del | novel | c.2413delN | p.Ile805TyrfsTer6 | p.I805Yfs*6 | Q3V6T2 | protein_coding | TCGA-FP-A4BE-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | ||
CCDC88A | deletion | Frame_Shift_Del | novel | c.1845delA | p.Glu616AsnfsTer33 | p.E616Nfs*33 | Q3V6T2 | protein_coding | TCGA-HU-A4GQ-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | ||
CCDC88A | SNV | Missense_Mutation | rs138449414 | c.5419N>A | p.Val1807Met | p.V1807M | Q3V6T2 | protein_coding | deleterious(0.02) | probably_damaging(0.998) | TCGA-EM-A22P-01 | Thyroid | thyroid carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
CCDC88A | SNV | Missense_Mutation | novel | c.528N>T | p.Met176Ile | p.M176I | Q3V6T2 | protein_coding | deleterious(0.02) | benign(0.012) | TCGA-H2-A26U-01 | Thyroid | thyroid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
CCDC88A | insertion | Frame_Shift_Ins | novel | c.3963_3964insCTCAAAAATATTTGTT | p.Glu1322LeufsTer6 | p.E1322Lfs*6 | Q3V6T2 | protein_coding | TCGA-FY-A4B0-01 | Thyroid | thyroid carcinoma | Male | >=65 | I/II | Hormone Therapy | synthroid | SD |
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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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