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Gene: ZCCHC3 |
Gene summary for ZCCHC3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ZCCHC3 | Gene ID | 85364 |
| Gene name | zinc finger CCHC-type containing 3 | |
| Gene Alias | C20orf99 | |
| Cytomap | 20p13 | |
| Gene Type | protein-coding | GO ID | GO:0001816 | UniProtAcc | Q9NUD5 |
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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 |
| 85364 | ZCCHC3 | HCC1_Meng | Human | Liver | HCC | 1.95e-39 | 4.77e-02 | 0.0246 |
| 85364 | ZCCHC3 | HCC2_Meng | Human | Liver | HCC | 3.80e-09 | 5.00e-02 | 0.0107 |
| 85364 | ZCCHC3 | HCC2 | Human | Liver | HCC | 2.63e-04 | 1.84e+00 | 0.5341 |
| 85364 | ZCCHC3 | S014 | Human | Liver | HCC | 1.79e-09 | 4.00e-01 | 0.2254 |
| 85364 | ZCCHC3 | S015 | Human | Liver | HCC | 2.57e-10 | 5.53e-01 | 0.2375 |
| 85364 | ZCCHC3 | S016 | Human | Liver | HCC | 2.02e-10 | 4.47e-01 | 0.2243 |
| 85364 | ZCCHC3 | S028 | Human | Liver | HCC | 7.74e-07 | 3.19e-01 | 0.2503 |
| 85364 | ZCCHC3 | S029 | Human | Liver | HCC | 2.17e-03 | 2.76e-01 | 0.2581 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:003052222 | Liver | HCC | intracellular receptor signaling pathway | 171/7958 | 265/18723 | 3.00e-13 | 1.61e-11 | 171 |
| GO:000961511 | Liver | HCC | response to virus | 210/7958 | 367/18723 | 7.32e-09 | 1.86e-07 | 210 |
| GO:0039528 | Liver | HCC | cytoplasmic pattern recognition receptor signaling pathway in response to virus | 30/7958 | 34/18723 | 3.88e-08 | 8.39e-07 | 30 |
| GO:00027533 | Liver | HCC | cytoplasmic pattern recognition receptor signaling pathway | 46/7958 | 60/18723 | 7.37e-08 | 1.49e-06 | 46 |
| GO:00022211 | Liver | HCC | pattern recognition receptor signaling pathway | 107/7958 | 172/18723 | 1.37e-07 | 2.58e-06 | 107 |
| GO:00395291 | Liver | HCC | RIG-I signaling pathway | 24/7958 | 27/18723 | 7.23e-07 | 1.12e-05 | 24 |
| GO:00516071 | Liver | HCC | defense response to virus | 151/7958 | 265/18723 | 1.27e-06 | 1.85e-05 | 151 |
| GO:01405461 | Liver | HCC | defense response to symbiont | 151/7958 | 265/18723 | 1.27e-06 | 1.85e-05 | 151 |
| GO:00985861 | Liver | HCC | cellular response to virus | 57/7958 | 84/18723 | 2.30e-06 | 3.11e-05 | 57 |
| GO:00324814 | Liver | HCC | positive regulation of type I interferon production | 41/7958 | 58/18723 | 1.29e-05 | 1.44e-04 | 41 |
| GO:0032479 | Liver | HCC | regulation of type I interferon production | 60/7958 | 95/18723 | 3.84e-05 | 3.80e-04 | 60 |
| GO:0032606 | Liver | HCC | type I interferon production | 60/7958 | 95/18723 | 3.84e-05 | 3.80e-04 | 60 |
| GO:0039531 | Liver | HCC | regulation of viral-induced cytoplasmic pattern recognition receptor signaling pathway | 20/7958 | 24/18723 | 4.92e-05 | 4.70e-04 | 20 |
| GO:00028312 | Liver | HCC | regulation of response to biotic stimulus | 173/7958 | 327/18723 | 8.55e-05 | 7.48e-04 | 173 |
| GO:00395351 | Liver | HCC | regulation of RIG-I signaling pathway | 17/7958 | 20/18723 | 1.18e-04 | 9.87e-04 | 17 |
| GO:00622072 | Liver | HCC | regulation of pattern recognition receptor signaling pathway | 59/7958 | 105/18723 | 3.18e-03 | 1.47e-02 | 59 |
| GO:00450881 | Liver | HCC | regulation of innate immune response | 113/7958 | 218/18723 | 3.27e-03 | 1.50e-02 | 113 |
| GO:0071359 | Liver | HCC | cellular response to dsRNA | 16/7958 | 22/18723 | 4.03e-03 | 1.76e-02 | 16 |
| GO:0002218 | Liver | HCC | activation of innate immune response | 32/7958 | 52/18723 | 4.35e-03 | 1.89e-02 | 32 |
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| 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 |
| ZCCHC3 | SNV | Missense_Mutation | novel | c.1141N>T | p.Ala381Ser | p.A381S | Q9NUD5 | protein_coding | tolerated(0.31) | benign(0.102) | TCGA-OL-A5RZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
| ZCCHC3 | SNV | Missense_Mutation | novel | c.307N>C | p.Asp103His | p.D103H | Q9NUD5 | protein_coding | deleterious(0.01) | possibly_damaging(0.642) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ZCCHC3 | SNV | Missense_Mutation | novel | c.951N>A | p.Phe317Leu | p.F317L | Q9NUD5 | protein_coding | tolerated(0.24) | benign(0.259) | TCGA-AY-6386-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fu | SD |
| ZCCHC3 | SNV | Missense_Mutation | novel | c.736G>T | p.Gly246Trp | p.G246W | Q9NUD5 | protein_coding | deleterious(0.02) | possibly_damaging(0.782) | TCGA-DM-A1HB-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| ZCCHC3 | SNV | Missense_Mutation | novel | c.1138N>G | p.His380Asp | p.H380D | Q9NUD5 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ZCCHC3 | SNV | Missense_Mutation | novel | c.766N>C | p.Phe256Leu | p.F256L | Q9NUD5 | protein_coding | tolerated(0.74) | benign(0.254) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD |
| ZCCHC3 | SNV | Missense_Mutation | novel | c.673T>C | p.Phe225Leu | p.F225L | Q9NUD5 | protein_coding | deleterious(0.01) | probably_damaging(0.987) | TCGA-BS-A0UF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| ZCCHC3 | SNV | Missense_Mutation | novel | c.140N>C | p.Leu47Pro | p.L47P | Q9NUD5 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.81) | TCGA-DD-AADR-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| ZCCHC3 | SNV | Missense_Mutation | novel | c.637N>T | p.Asp213Tyr | p.D213Y | Q9NUD5 | protein_coding | deleterious(0) | possibly_damaging(0.791) | TCGA-05-4390-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| ZCCHC3 | SNV | Missense_Mutation | rs542196827 | c.567N>G | p.Ile189Met | p.I189M | Q9NUD5 | protein_coding | deleterious(0.01) | probably_damaging(0.951) | TCGA-50-5049-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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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