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Gene: CYC1 |
Gene summary for CYC1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CYC1 | Gene ID | 1537 |
| Gene name | cytochrome c1 | |
| Gene Alias | MC3DN6 | |
| Cytomap | 8q24.3 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | P08574 |
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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 |
| 1537 | CYC1 | GSM4909281 | Human | Breast | IDC | 5.62e-43 | 7.70e-01 | 0.21 |
| 1537 | CYC1 | GSM4909282 | Human | Breast | IDC | 4.89e-29 | 5.68e-01 | -0.0288 |
| 1537 | CYC1 | GSM4909285 | Human | Breast | IDC | 5.89e-32 | 7.48e-01 | 0.21 |
| 1537 | CYC1 | GSM4909294 | Human | Breast | IDC | 2.05e-02 | 6.77e-02 | 0.2022 |
| 1537 | CYC1 | GSM4909296 | Human | Breast | IDC | 9.31e-18 | 2.93e-01 | 0.1524 |
| 1537 | CYC1 | GSM4909297 | Human | Breast | IDC | 2.49e-15 | 3.85e-02 | 0.1517 |
| 1537 | CYC1 | GSM4909304 | Human | Breast | IDC | 6.39e-05 | 3.05e-01 | 0.1636 |
| 1537 | CYC1 | GSM4909306 | Human | Breast | IDC | 1.42e-20 | 5.52e-01 | 0.1564 |
| 1537 | CYC1 | GSM4909307 | Human | Breast | IDC | 4.23e-05 | 2.92e-01 | 0.1569 |
| 1537 | CYC1 | GSM4909308 | Human | Breast | IDC | 9.31e-04 | 3.69e-01 | 0.158 |
| 1537 | CYC1 | GSM4909309 | Human | Breast | IDC | 6.42e-08 | 2.39e-01 | 0.0483 |
| 1537 | CYC1 | GSM4909311 | Human | Breast | IDC | 6.68e-41 | 2.49e-01 | 0.1534 |
| 1537 | CYC1 | GSM4909312 | Human | Breast | IDC | 1.23e-20 | 3.52e-01 | 0.1552 |
| 1537 | CYC1 | GSM4909313 | Human | Breast | IDC | 1.26e-02 | -7.37e-02 | 0.0391 |
| 1537 | CYC1 | GSM4909317 | Human | Breast | IDC | 3.36e-06 | 4.22e-01 | 0.1355 |
| 1537 | CYC1 | GSM4909319 | Human | Breast | IDC | 1.67e-53 | 2.96e-01 | 0.1563 |
| 1537 | CYC1 | GSM4909320 | Human | Breast | IDC | 1.54e-07 | 1.69e-01 | 0.1575 |
| 1537 | CYC1 | GSM4909321 | Human | Breast | IDC | 3.68e-32 | 4.29e-01 | 0.1559 |
| 1537 | CYC1 | brca1 | Human | Breast | Precancer | 1.12e-28 | 6.19e-01 | -0.0338 |
| 1537 | CYC1 | brca2 | Human | Breast | Precancer | 6.13e-09 | 3.65e-01 | -0.024 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:00453337 | Liver | Cirrhotic | cellular respiration | 122/4634 | 230/18723 | 2.15e-20 | 6.43e-18 | 122 |
| GO:001598012 | Liver | Cirrhotic | energy derivation by oxidation of organic compounds | 154/4634 | 318/18723 | 3.11e-20 | 8.87e-18 | 154 |
| GO:00061197 | Liver | Cirrhotic | oxidative phosphorylation | 86/4634 | 141/18723 | 6.08e-20 | 1.66e-17 | 86 |
| GO:004343412 | Liver | Cirrhotic | response to peptide hormone | 149/4634 | 414/18723 | 1.70e-07 | 4.49e-06 | 149 |
| GO:00061227 | Liver | Cirrhotic | mitochondrial electron transport, ubiquinol to cytochrome c | 10/4634 | 11/18723 | 7.30e-06 | 1.13e-04 | 10 |
| GO:000609122 | Liver | HCC | generation of precursor metabolites and energy | 340/7958 | 490/18723 | 4.04e-34 | 2.85e-31 | 340 |
| GO:000906012 | Liver | HCC | aerobic respiration | 147/7958 | 189/18723 | 3.13e-23 | 6.61e-21 | 147 |
| GO:004533312 | Liver | HCC | cellular respiration | 171/7958 | 230/18723 | 6.35e-23 | 1.26e-20 | 171 |
| GO:004603422 | Liver | HCC | ATP metabolic process | 198/7958 | 277/18723 | 8.30e-23 | 1.55e-20 | 198 |
| GO:001598022 | Liver | HCC | energy derivation by oxidation of organic compounds | 221/7958 | 318/18723 | 1.02e-22 | 1.86e-20 | 221 |
| GO:002290022 | Liver | HCC | electron transport chain | 134/7958 | 175/18723 | 3.32e-20 | 4.68e-18 | 134 |
| GO:000611912 | Liver | HCC | oxidative phosphorylation | 110/7958 | 141/18723 | 6.58e-18 | 7.45e-16 | 110 |
| GO:002290412 | Liver | HCC | respiratory electron transport chain | 89/7958 | 114/18723 | 8.68e-15 | 5.73e-13 | 89 |
| GO:004343422 | Liver | HCC | response to peptide hormone | 247/7958 | 414/18723 | 9.55e-13 | 4.77e-11 | 247 |
| GO:004277312 | Liver | HCC | ATP synthesis coupled electron transport | 74/7958 | 95/18723 | 1.94e-12 | 9.18e-11 | 74 |
| GO:004277512 | Liver | HCC | mitochondrial ATP synthesis coupled electron transport | 74/7958 | 95/18723 | 1.94e-12 | 9.18e-11 | 74 |
| GO:001964612 | Liver | HCC | aerobic electron transport chain | 67/7958 | 87/18723 | 5.43e-11 | 2.00e-09 | 67 |
| GO:19026007 | Liver | HCC | proton transmembrane transport | 87/7958 | 157/18723 | 7.27e-04 | 4.42e-03 | 87 |
| GO:000612212 | Liver | HCC | mitochondrial electron transport, ubiquinol to cytochrome c | 10/7958 | 11/18723 | 1.30e-03 | 7.01e-03 | 10 |
| GO:002290018 | Oral cavity | OSCC | electron transport chain | 126/7305 | 175/18723 | 6.65e-19 | 8.42e-17 | 126 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0501218 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
| hsa0502016 | Breast | Precancer | Prion disease | 95/684 | 273/8465 | 1.39e-37 | 1.46e-35 | 1.12e-35 | 95 |
| hsa0501616 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0019016 | Breast | Precancer | Oxidative phosphorylation | 59/684 | 134/8465 | 6.15e-30 | 3.24e-28 | 2.48e-28 | 59 |
| hsa0501016 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
| hsa0501416 | Breast | Precancer | Amyotrophic lateral sclerosis | 98/684 | 364/8465 | 2.13e-28 | 8.41e-27 | 6.44e-27 | 98 |
| hsa0502216 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
| hsa0520818 | Breast | Precancer | Chemical carcinogenesis - reactive oxygen species | 68/684 | 223/8465 | 3.61e-23 | 1.14e-21 | 8.73e-22 | 68 |
| hsa0471418 | Breast | Precancer | Thermogenesis | 68/684 | 232/8465 | 4.40e-22 | 1.26e-20 | 9.69e-21 | 68 |
| hsa0541518 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
| hsa0493216 | Breast | Precancer | Non-alcoholic fatty liver disease | 48/684 | 155/8465 | 6.16e-17 | 1.50e-15 | 1.15e-15 | 48 |
| hsa0426016 | Breast | Precancer | Cardiac muscle contraction | 22/684 | 87/8465 | 9.72e-07 | 1.62e-05 | 1.24e-05 | 22 |
| hsa0501219 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
| hsa0502017 | Breast | Precancer | Prion disease | 95/684 | 273/8465 | 1.39e-37 | 1.46e-35 | 1.12e-35 | 95 |
| hsa0501617 | Breast | Precancer | Huntington disease | 98/684 | 306/8465 | 2.85e-35 | 2.25e-33 | 1.72e-33 | 98 |
| hsa0019017 | Breast | Precancer | Oxidative phosphorylation | 59/684 | 134/8465 | 6.15e-30 | 3.24e-28 | 2.48e-28 | 59 |
| hsa0501017 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
| hsa0501417 | Breast | Precancer | Amyotrophic lateral sclerosis | 98/684 | 364/8465 | 2.13e-28 | 8.41e-27 | 6.44e-27 | 98 |
| hsa0502217 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
| hsa0520819 | Breast | Precancer | Chemical carcinogenesis - reactive oxygen species | 68/684 | 223/8465 | 3.61e-23 | 1.14e-21 | 8.73e-22 | 68 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 |
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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 |
| CYC1 | SNV | Missense_Mutation | c.854N>A | p.Arg285Gln | p.R285Q | P08574 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CYC1 | SNV | Missense_Mutation | c.488A>C | p.Glu163Ala | p.E163A | P08574 | protein_coding | tolerated(0.05) | benign(0.031) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| CYC1 | SNV | Missense_Mutation | novel | c.357G>T | p.Gln119His | p.Q119H | P08574 | protein_coding | deleterious(0) | probably_damaging(0.95) | TCGA-D5-6530-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| CYC1 | deletion | Frame_Shift_Del | c.276delC | p.Ser93AlafsTer161 | p.S93Afs*161 | P08574 | protein_coding | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD | |||
| CYC1 | insertion | Frame_Shift_Ins | novel | c.758_759insA | p.Glu254ArgfsTer3 | p.E254Rfs*3 | P08574 | protein_coding | TCGA-CA-6719-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | ||
| CYC1 | deletion | Frame_Shift_Del | c.270delN | p.Ser93AlafsTer161 | p.S93Afs*161 | P08574 | protein_coding | TCGA-CM-6171-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| CYC1 | insertion | Frame_Shift_Ins | rs756254049 | c.269_270insC | p.Ser93GlnfsTer26 | p.S93Qfs*26 | P08574 | protein_coding | TCGA-G4-6586-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| CYC1 | deletion | Frame_Shift_Del | c.276delC | p.Ser93AlafsTer161 | p.S93Afs*161 | P08574 | protein_coding | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| CYC1 | SNV | Missense_Mutation | c.608N>T | p.Ala203Val | p.A203V | P08574 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CYC1 | SNV | Missense_Mutation | rs749437250 | c.601N>A | p.Val201Met | p.V201M | P08574 | protein_coding | deleterious(0.01) | benign(0.281) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD |
| Page: 1 2 3 4 5 6 |
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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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