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Gene: SURF1 |
Gene summary for SURF1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SURF1 | Gene ID | 6834 |
| Gene name | SURF1 cytochrome c oxidase assembly factor | |
| Gene Alias | CMT4K | |
| Cytomap | 9q34.2 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | A0A087WYS9 |
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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 |
| 6834 | SURF1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.41e-02 | 1.42e-01 | 0.0155 |
| 6834 | SURF1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 6.28e-08 | 3.73e-01 | -0.1808 |
| 6834 | SURF1 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.21e-13 | 3.71e-01 | -0.1954 |
| 6834 | SURF1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.40e-06 | 5.98e-01 | -0.2196 |
| 6834 | SURF1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 5.61e-06 | 2.83e-01 | -0.1207 |
| 6834 | SURF1 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.48e-02 | 3.10e-01 | -0.1526 |
| 6834 | SURF1 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.12e-12 | 3.62e-01 | -0.1464 |
| 6834 | SURF1 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.47e-03 | 1.84e-01 | -0.1001 |
| 6834 | SURF1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.93e-09 | 3.73e-01 | -0.059 |
| 6834 | SURF1 | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.66e-02 | 3.46e-01 | -0.2061 |
| 6834 | SURF1 | HTA11_5216_2000001011 | Human | Colorectum | SER | 4.63e-04 | 4.78e-01 | -0.1462 |
| 6834 | SURF1 | HTA11_546_2000001011 | Human | Colorectum | AD | 3.21e-05 | 3.38e-01 | -0.0842 |
| 6834 | SURF1 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.69e-07 | 2.83e-01 | 0.096 |
| 6834 | SURF1 | HTA11_10623_2000001011 | Human | Colorectum | AD | 8.48e-07 | 4.33e-01 | -0.0177 |
| 6834 | SURF1 | HTA11_6801_2000001011 | Human | Colorectum | SER | 1.45e-04 | 3.79e-01 | 0.0171 |
| 6834 | SURF1 | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.87e-03 | 2.03e-01 | 0.0338 |
| 6834 | SURF1 | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.74e-08 | 2.69e-01 | 0.0674 |
| 6834 | SURF1 | HTA11_6818_2000001021 | Human | Colorectum | AD | 3.37e-02 | 3.07e-01 | 0.0588 |
| 6834 | SURF1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.57e-08 | 2.72e-01 | 0.3859 |
| 6834 | SURF1 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 7.59e-12 | 3.49e-01 | 0.3005 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| 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:0006091 | Colorectum | AD | generation of precursor metabolites and energy | 209/3918 | 490/18723 | 3.17e-28 | 6.61e-25 | 209 |
| GO:0009060 | Colorectum | AD | aerobic respiration | 108/3918 | 189/18723 | 9.14e-28 | 1.43e-24 | 108 |
| GO:0045333 | Colorectum | AD | cellular respiration | 119/3918 | 230/18723 | 3.21e-25 | 4.02e-22 | 119 |
| GO:0015980 | Colorectum | AD | energy derivation by oxidation of organic compounds | 143/3918 | 318/18723 | 2.78e-22 | 2.49e-19 | 143 |
| GO:0022900 | Colorectum | AD | electron transport chain | 89/3918 | 175/18723 | 1.42e-18 | 8.91e-16 | 89 |
| GO:0033108 | Colorectum | AD | mitochondrial respiratory chain complex assembly | 46/3918 | 93/18723 | 8.95e-10 | 6.91e-08 | 46 |
| GO:1902600 | Colorectum | AD | proton transmembrane transport | 66/3918 | 157/18723 | 1.59e-09 | 1.17e-07 | 66 |
| GO:00090601 | Colorectum | SER | aerobic respiration | 96/2897 | 189/18723 | 5.53e-30 | 1.70e-26 | 96 |
| GO:00453331 | Colorectum | SER | cellular respiration | 103/2897 | 230/18723 | 2.35e-26 | 3.61e-23 | 103 |
| GO:00060911 | Colorectum | SER | generation of precursor metabolites and energy | 168/2897 | 490/18723 | 1.39e-25 | 1.70e-22 | 168 |
| GO:00159801 | Colorectum | SER | energy derivation by oxidation of organic compounds | 119/2897 | 318/18723 | 5.28e-22 | 4.62e-19 | 119 |
| GO:00229001 | Colorectum | SER | electron transport chain | 77/2897 | 175/18723 | 1.77e-19 | 1.36e-16 | 77 |
| GO:19026001 | Colorectum | SER | proton transmembrane transport | 60/2897 | 157/18723 | 3.12e-12 | 7.08e-10 | 60 |
| GO:00331081 | Colorectum | SER | mitochondrial respiratory chain complex assembly | 39/2897 | 93/18723 | 8.13e-10 | 8.74e-08 | 39 |
| GO:00090602 | Colorectum | MSS | aerobic respiration | 98/3467 | 189/18723 | 3.35e-25 | 1.05e-21 | 98 |
| GO:00060912 | Colorectum | MSS | generation of precursor metabolites and energy | 186/3467 | 490/18723 | 1.14e-24 | 2.15e-21 | 186 |
| GO:00453332 | Colorectum | MSS | cellular respiration | 107/3467 | 230/18723 | 1.64e-22 | 2.05e-19 | 107 |
| GO:00159802 | Colorectum | MSS | energy derivation by oxidation of organic compounds | 131/3467 | 318/18723 | 2.60e-21 | 2.70e-18 | 131 |
| GO:00229002 | Colorectum | MSS | electron transport chain | 83/3467 | 175/18723 | 2.06e-18 | 1.17e-15 | 83 |
| GO:00331082 | Colorectum | MSS | mitochondrial respiratory chain complex assembly | 44/3467 | 93/18723 | 2.17e-10 | 2.09e-08 | 44 |
| Page: 1 2 3 4 5 6 |
| 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 |
| SURF1 | insertion | Frame_Shift_Ins | novel | c.651_652insACCCAACGTAAAGGCCATACAGGACT | p.Pro218ThrfsTer59 | p.P218Tfs*59 | Q15526 | protein_coding | TCGA-B6-A0IA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| SURF1 | SNV | Missense_Mutation | rs782044026 | c.251N>A | p.Arg84Gln | p.R84Q | Q15526 | protein_coding | deleterious(0.01) | probably_damaging(0.913) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SURF1 | SNV | Missense_Mutation | novel | c.667G>C | p.Glu223Gln | p.E223Q | Q15526 | protein_coding | tolerated(0.09) | benign(0.248) | TCGA-C5-A2LX-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| SURF1 | SNV | Missense_Mutation | novel | c.425N>T | p.Pro142Leu | p.P142L | Q15526 | protein_coding | deleterious(0) | possibly_damaging(0.811) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| SURF1 | SNV | Missense_Mutation | novel | c.689N>A | p.Arg230Gln | p.R230Q | Q15526 | protein_coding | deleterious(0) | probably_damaging(0.928) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| SURF1 | SNV | Missense_Mutation | rs782024654 | c.269T>C | p.Leu90Pro | p.L90P | Q15526 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AX-A2HJ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SURF1 | SNV | Missense_Mutation | rs374365243 | c.250N>T | p.Arg84Trp | p.R84W | Q15526 | protein_coding | tolerated(0.1) | benign(0.333) | TCGA-AX-A3FT-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SURF1 | SNV | Missense_Mutation | c.647N>C | p.Phe216Ser | p.F216S | Q15526 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SURF1 | SNV | Missense_Mutation | novel | c.886N>A | p.Gly296Arg | p.G296R | Q15526 | protein_coding | tolerated(1) | benign(0) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SURF1 | SNV | Missense_Mutation | rs782453666 | c.184N>A | p.Leu62Ile | p.L62I | Q15526 | protein_coding | deleterious(0.04) | benign(0.076) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
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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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