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Gene: MMS19 |
Gene summary for MMS19 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | MMS19 | Gene ID | 64210 |
| Gene name | MMS19 homolog, cytosolic iron-sulfur assembly component | |
| Gene Alias | CIAO4 | |
| Cytomap | 10q24.1 | |
| Gene Type | protein-coding | GO ID | GO:0000018 | UniProtAcc | Q96T76 |
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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 |
| 64210 | MMS19 | LZE4T | Human | Esophagus | ESCC | 2.25e-02 | 8.88e-02 | 0.0811 |
| 64210 | MMS19 | LZE8T | Human | Esophagus | ESCC | 2.53e-07 | 1.27e-01 | 0.067 |
| 64210 | MMS19 | LZE24T | Human | Esophagus | ESCC | 6.69e-13 | 2.87e-01 | 0.0596 |
| 64210 | MMS19 | P1T-E | Human | Esophagus | ESCC | 3.19e-02 | 9.16e-02 | 0.0875 |
| 64210 | MMS19 | P2T-E | Human | Esophagus | ESCC | 6.02e-24 | 2.72e-01 | 0.1177 |
| 64210 | MMS19 | P4T-E | Human | Esophagus | ESCC | 3.02e-13 | 2.78e-01 | 0.1323 |
| 64210 | MMS19 | P5T-E | Human | Esophagus | ESCC | 1.08e-08 | 1.36e-01 | 0.1327 |
| 64210 | MMS19 | P8T-E | Human | Esophagus | ESCC | 4.64e-15 | 2.28e-01 | 0.0889 |
| 64210 | MMS19 | P9T-E | Human | Esophagus | ESCC | 5.58e-06 | 1.35e-01 | 0.1131 |
| 64210 | MMS19 | P10T-E | Human | Esophagus | ESCC | 7.84e-11 | 7.56e-02 | 0.116 |
| 64210 | MMS19 | P11T-E | Human | Esophagus | ESCC | 1.35e-06 | 2.07e-01 | 0.1426 |
| 64210 | MMS19 | P12T-E | Human | Esophagus | ESCC | 4.01e-25 | 3.87e-01 | 0.1122 |
| 64210 | MMS19 | P15T-E | Human | Esophagus | ESCC | 4.24e-19 | 3.70e-01 | 0.1149 |
| 64210 | MMS19 | P16T-E | Human | Esophagus | ESCC | 1.90e-25 | 3.76e-01 | 0.1153 |
| 64210 | MMS19 | P17T-E | Human | Esophagus | ESCC | 5.50e-03 | 2.11e-01 | 0.1278 |
| 64210 | MMS19 | P19T-E | Human | Esophagus | ESCC | 5.26e-09 | 3.89e-01 | 0.1662 |
| 64210 | MMS19 | P20T-E | Human | Esophagus | ESCC | 7.98e-10 | 1.83e-01 | 0.1124 |
| 64210 | MMS19 | P21T-E | Human | Esophagus | ESCC | 1.84e-17 | 2.61e-01 | 0.1617 |
| 64210 | MMS19 | P22T-E | Human | Esophagus | ESCC | 1.79e-09 | 1.20e-01 | 0.1236 |
| 64210 | MMS19 | P23T-E | Human | Esophagus | ESCC | 7.55e-18 | 3.58e-01 | 0.108 |
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| 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 |
| ∗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:00067905 | Oral cavity | OSCC | sulfur compound metabolic process | 168/7305 | 339/18723 | 4.50e-05 | 3.84e-04 | 168 |
| GO:00457394 | Oral cavity | OSCC | positive regulation of DNA repair | 45/7305 | 73/18723 | 7.46e-05 | 5.82e-04 | 45 |
| GO:0006289 | Oral cavity | OSCC | nucleotide-excision repair | 37/7305 | 60/18723 | 3.15e-04 | 1.96e-03 | 37 |
| GO:00162262 | Oral cavity | OSCC | iron-sulfur cluster assembly | 19/7305 | 26/18723 | 4.46e-04 | 2.70e-03 | 19 |
| GO:00311632 | Oral cavity | OSCC | metallo-sulfur cluster assembly | 19/7305 | 26/18723 | 4.46e-04 | 2.70e-03 | 19 |
| GO:0006310 | Oral cavity | OSCC | DNA recombination | 147/7305 | 305/18723 | 6.33e-04 | 3.56e-03 | 147 |
| GO:20007792 | Oral cavity | OSCC | regulation of double-strand break repair | 48/7305 | 85/18723 | 8.14e-04 | 4.35e-03 | 48 |
| GO:0000725 | Oral cavity | OSCC | recombinational repair | 70/7305 | 140/18723 | 5.22e-03 | 2.03e-02 | 70 |
| GO:0000724 | Oral cavity | OSCC | double-strand break repair via homologous recombination | 69/7305 | 138/18723 | 5.52e-03 | 2.14e-02 | 69 |
| GO:2000781 | Oral cavity | OSCC | positive regulation of double-strand break repair | 23/7305 | 40/18723 | 1.36e-02 | 4.50e-02 | 23 |
| GO:0097428 | Oral cavity | OSCC | protein maturation by iron-sulfur cluster transfer | 11/7305 | 16/18723 | 1.56e-02 | 4.99e-02 | 11 |
| GO:005105222 | Oral cavity | EOLP | regulation of DNA metabolic process | 75/2218 | 359/18723 | 5.81e-07 | 1.53e-05 | 75 |
| GO:005105421 | Oral cavity | EOLP | positive regulation of DNA metabolic process | 45/2218 | 201/18723 | 1.68e-05 | 2.77e-04 | 45 |
| GO:200102024 | Oral cavity | EOLP | regulation of response to DNA damage stimulus | 47/2218 | 219/18723 | 3.47e-05 | 4.85e-04 | 47 |
| GO:200102213 | Oral cavity | EOLP | positive regulation of response to DNA damage stimulus | 23/2218 | 105/18723 | 2.44e-03 | 1.49e-02 | 23 |
| GO:00063022 | Oral cavity | EOLP | double-strand break repair | 44/2218 | 251/18723 | 4.94e-03 | 2.62e-02 | 44 |
| GO:005160423 | Oral cavity | EOLP | protein maturation | 50/2218 | 294/18723 | 5.32e-03 | 2.77e-02 | 50 |
| GO:20007811 | Oral cavity | EOLP | positive regulation of double-strand break repair | 11/2218 | 40/18723 | 5.53e-03 | 2.86e-02 | 11 |
| GO:20007791 | Oral cavity | EOLP | regulation of double-strand break repair | 18/2218 | 85/18723 | 9.81e-03 | 4.43e-02 | 18 |
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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 |
| 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 |
| MMS19 | SNV | Missense_Mutation | c.2980N>G | p.Pro994Ala | p.P994A | Q96T76 | protein_coding | tolerated(1) | benign(0) | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| MMS19 | SNV | Missense_Mutation | rs756307565 | c.2575N>A | p.Glu859Lys | p.E859K | Q96T76 | protein_coding | tolerated(0.16) | benign(0.003) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| MMS19 | SNV | Missense_Mutation | novel | c.781N>T | p.Pro261Ser | p.P261S | Q96T76 | protein_coding | deleterious(0.04) | probably_damaging(1) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| MMS19 | SNV | Missense_Mutation | c.2399N>T | p.Thr800Ile | p.T800I | Q96T76 | protein_coding | deleterious(0.02) | benign(0.131) | TCGA-AR-A0TU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Doxorubicin | SD | |
| MMS19 | insertion | Frame_Shift_Ins | novel | c.209_210insT | p.Gln70HisfsTer27 | p.Q70Hfs*27 | Q96T76 | protein_coding | TCGA-BH-A0BD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| MMS19 | insertion | Nonsense_Mutation | novel | c.208_209insCCTTGACATAACTGGG | p.Gln70ProfsTer4 | p.Q70Pfs*4 | Q96T76 | protein_coding | TCGA-BH-A0BD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
| MMS19 | SNV | Missense_Mutation | novel | c.2401N>G | p.Leu801Val | p.L801V | Q96T76 | protein_coding | tolerated(0.07) | benign(0.119) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
| MMS19 | SNV | Missense_Mutation | c.952N>A | p.Glu318Lys | p.E318K | Q96T76 | protein_coding | deleterious(0) | probably_damaging(0.954) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| MMS19 | SNV | Missense_Mutation | c.1988N>T | p.Thr663Ile | p.T663I | Q96T76 | protein_coding | tolerated(0.08) | possibly_damaging(0.572) | TCGA-AA-3688-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
| MMS19 | SNV | Missense_Mutation | novel | c.2391G>T | p.Gln797His | p.Q797H | Q96T76 | protein_coding | deleterious(0) | benign(0.219) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | 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 |
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