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Gene: CHCHD4 |
Gene summary for CHCHD4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CHCHD4 | Gene ID | 131474 |
| Gene name | coiled-coil-helix-coiled-coil-helix domain containing 4 | |
| Gene Alias | MIA40 | |
| Cytomap | 3p25.1 | |
| Gene Type | protein-coding | GO ID | GO:0006457 | UniProtAcc | A0A024R2I5 |
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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 |
| 131474 | CHCHD4 | LZE4T | Human | Esophagus | ESCC | 2.18e-06 | 1.03e-01 | 0.0811 |
| 131474 | CHCHD4 | LZE8T | Human | Esophagus | ESCC | 4.92e-02 | 5.97e-02 | 0.067 |
| 131474 | CHCHD4 | LZE24T | Human | Esophagus | ESCC | 6.48e-03 | 5.35e-02 | 0.0596 |
| 131474 | CHCHD4 | P1T-E | Human | Esophagus | ESCC | 1.33e-02 | 1.46e-01 | 0.0875 |
| 131474 | CHCHD4 | P2T-E | Human | Esophagus | ESCC | 3.53e-07 | 1.66e-01 | 0.1177 |
| 131474 | CHCHD4 | P4T-E | Human | Esophagus | ESCC | 4.76e-13 | 3.54e-01 | 0.1323 |
| 131474 | CHCHD4 | P5T-E | Human | Esophagus | ESCC | 1.23e-26 | 6.06e-01 | 0.1327 |
| 131474 | CHCHD4 | P8T-E | Human | Esophagus | ESCC | 4.14e-10 | 1.13e-01 | 0.0889 |
| 131474 | CHCHD4 | P9T-E | Human | Esophagus | ESCC | 7.54e-13 | 2.21e-01 | 0.1131 |
| 131474 | CHCHD4 | P10T-E | Human | Esophagus | ESCC | 1.26e-15 | 1.20e-01 | 0.116 |
| 131474 | CHCHD4 | P11T-E | Human | Esophagus | ESCC | 3.36e-09 | 2.97e-01 | 0.1426 |
| 131474 | CHCHD4 | P12T-E | Human | Esophagus | ESCC | 8.59e-12 | 2.72e-01 | 0.1122 |
| 131474 | CHCHD4 | P15T-E | Human | Esophagus | ESCC | 2.35e-10 | 1.02e-01 | 0.1149 |
| 131474 | CHCHD4 | P16T-E | Human | Esophagus | ESCC | 1.56e-07 | 1.69e-01 | 0.1153 |
| 131474 | CHCHD4 | P17T-E | Human | Esophagus | ESCC | 4.59e-07 | 2.61e-01 | 0.1278 |
| 131474 | CHCHD4 | P20T-E | Human | Esophagus | ESCC | 3.05e-11 | 2.64e-01 | 0.1124 |
| 131474 | CHCHD4 | P21T-E | Human | Esophagus | ESCC | 1.19e-20 | 4.20e-01 | 0.1617 |
| 131474 | CHCHD4 | P22T-E | Human | Esophagus | ESCC | 4.93e-13 | 1.60e-01 | 0.1236 |
| 131474 | CHCHD4 | P23T-E | Human | Esophagus | ESCC | 4.15e-13 | 3.12e-01 | 0.108 |
| 131474 | CHCHD4 | P24T-E | Human | Esophagus | ESCC | 6.69e-15 | 3.11e-01 | 0.1287 |
| Page: 1 2 3 4 5 |
| 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 | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:0072594110 | Esophagus | ESCC | establishment of protein localization to organelle | 311/8552 | 422/18723 | 3.02e-32 | 2.13e-29 | 311 |
| GO:0006605111 | Esophagus | ESCC | protein targeting | 229/8552 | 314/18723 | 4.93e-23 | 1.01e-20 | 229 |
| GO:0006457110 | Esophagus | ESCC | protein folding | 163/8552 | 212/18723 | 1.13e-20 | 1.74e-18 | 163 |
| GO:0006839110 | Esophagus | ESCC | mitochondrial transport | 187/8552 | 254/18723 | 8.35e-20 | 9.81e-18 | 187 |
| GO:0033108110 | Esophagus | ESCC | mitochondrial respiratory chain complex assembly | 83/8552 | 93/18723 | 9.56e-19 | 1.05e-16 | 83 |
| GO:0072655110 | Esophagus | ESCC | establishment of protein localization to mitochondrion | 97/8552 | 120/18723 | 2.17e-15 | 1.33e-13 | 97 |
| GO:0070585110 | Esophagus | ESCC | protein localization to mitochondrion | 100/8552 | 125/18723 | 2.96e-15 | 1.77e-13 | 100 |
| GO:001703818 | Esophagus | ESCC | protein import | 149/8552 | 206/18723 | 5.90e-15 | 3.31e-13 | 149 |
| GO:0006626110 | Esophagus | ESCC | protein targeting to mitochondrion | 81/8552 | 100/18723 | 3.60e-13 | 1.67e-11 | 81 |
| GO:005160418 | Esophagus | ESCC | protein maturation | 189/8552 | 294/18723 | 7.64e-11 | 2.39e-09 | 189 |
| GO:00718069 | Esophagus | ESCC | protein transmembrane transport | 47/8552 | 59/18723 | 9.02e-08 | 1.51e-06 | 47 |
| GO:0006458110 | Esophagus | ESCC | 'de novo' protein folding | 36/8552 | 43/18723 | 2.90e-07 | 4.20e-06 | 36 |
| GO:1990542110 | Esophagus | ESCC | mitochondrial transmembrane transport | 72/8552 | 102/18723 | 2.94e-07 | 4.23e-06 | 72 |
| GO:00650026 | Esophagus | ESCC | intracellular protein transmembrane transport | 40/8552 | 51/18723 | 1.76e-06 | 2.08e-05 | 40 |
| GO:0051084110 | Esophagus | ESCC | 'de novo' posttranslational protein folding | 32/8552 | 39/18723 | 3.27e-06 | 3.65e-05 | 32 |
| GO:00447433 | Esophagus | ESCC | protein transmembrane import into intracellular organelle | 29/8552 | 36/18723 | 1.91e-05 | 1.67e-04 | 29 |
| GO:007259422 | Liver | HCC | establishment of protein localization to organelle | 299/7958 | 422/18723 | 1.06e-32 | 6.10e-30 | 299 |
| GO:000660512 | Liver | HCC | protein targeting | 219/7958 | 314/18723 | 7.74e-23 | 1.49e-20 | 219 |
| GO:000645712 | Liver | HCC | protein folding | 160/7958 | 212/18723 | 1.07e-22 | 1.88e-20 | 160 |
| GO:000683912 | Liver | HCC | mitochondrial transport | 184/7958 | 254/18723 | 2.30e-22 | 3.83e-20 | 184 |
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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 |
| CHCHD4 | SNV | Missense_Mutation | rs773338809 | c.313N>T | p.Arg105Trp | p.R105W | Q8N4Q1 | protein_coding | tolerated(0.16) | benign(0.013) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CHCHD4 | SNV | Missense_Mutation | c.11N>T | p.Ser4Leu | p.S4L | Q8N4Q1 | protein_coding | tolerated_low_confidence(0.09) | benign(0) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| CHCHD4 | SNV | Missense_Mutation | novel | c.257N>T | p.Ser86Phe | p.S86F | Q8N4Q1 | protein_coding | deleterious(0.04) | probably_damaging(0.999) | TCGA-AJ-A2QO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CHCHD4 | SNV | Missense_Mutation | novel | c.166N>C | p.Ile56Leu | p.I56L | Q8N4Q1 | protein_coding | tolerated(0.06) | benign(0.367) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| CHCHD4 | SNV | Missense_Mutation | rs755009391 | c.71N>A | p.Arg24Gln | p.R24Q | Q8N4Q1 | protein_coding | tolerated(0.29) | benign(0.024) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CHCHD4 | SNV | Missense_Mutation | novel | c.327A>C | p.Glu109Asp | p.E109D | Q8N4Q1 | protein_coding | tolerated(0.17) | possibly_damaging(0.716) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CHCHD4 | SNV | Missense_Mutation | rs755009391 | c.71N>A | p.Arg24Gln | p.R24Q | Q8N4Q1 | protein_coding | tolerated(0.29) | benign(0.024) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| CHCHD4 | SNV | Missense_Mutation | rs755009391 | c.71N>A | p.Arg24Gln | p.R24Q | Q8N4Q1 | protein_coding | tolerated(0.29) | benign(0.024) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
| CHCHD4 | SNV | Missense_Mutation | rs755009391 | c.71N>A | p.Arg24Gln | p.R24Q | Q8N4Q1 | protein_coding | tolerated(0.29) | benign(0.024) | TCGA-DF-A2KV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| CHCHD4 | SNV | Missense_Mutation | rs750347112 | c.82G>A | p.Val28Ile | p.V28I | Q8N4Q1 | protein_coding | tolerated(0.07) | benign(0.107) | TCGA-EO-A3KX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | 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 |
| Page: 1 |
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