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Gene: ATP5F1 |
Gene summary for ATP5F1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | ATP5F1 | Gene ID | 515 |
| Gene name | ATP synthase peripheral stalk-membrane subunit b | |
| Gene Alias | ATP5F1 | |
| Cytomap | 1p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | P24539 |
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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 |
| 515 | ATP5F1 | GSM4909281 | Human | Breast | IDC | 3.80e-09 | -2.35e-01 | 0.21 |
| 515 | ATP5F1 | GSM4909282 | Human | Breast | IDC | 8.23e-09 | -2.35e-01 | -0.0288 |
| 515 | ATP5F1 | GSM4909285 | Human | Breast | IDC | 1.78e-08 | -2.35e-01 | 0.21 |
| 515 | ATP5F1 | GSM4909286 | Human | Breast | IDC | 3.80e-09 | -2.35e-01 | 0.1081 |
| 515 | ATP5F1 | GSM4909287 | Human | Breast | IDC | 5.28e-10 | -2.35e-01 | 0.2057 |
| 515 | ATP5F1 | GSM4909290 | Human | Breast | IDC | 1.13e-06 | -2.35e-01 | 0.2096 |
| 515 | ATP5F1 | GSM4909291 | Human | Breast | IDC | 4.38e-05 | -2.35e-01 | 0.1753 |
| 515 | ATP5F1 | GSM4909293 | Human | Breast | IDC | 1.75e-09 | -2.35e-01 | 0.1581 |
| 515 | ATP5F1 | GSM4909294 | Human | Breast | IDC | 3.80e-09 | -2.35e-01 | 0.2022 |
| 515 | ATP5F1 | GSM4909295 | Human | Breast | IDC | 1.25e-03 | -2.35e-01 | 0.0898 |
| 515 | ATP5F1 | GSM4909296 | Human | Breast | IDC | 1.78e-08 | -2.35e-01 | 0.1524 |
| 515 | ATP5F1 | GSM4909297 | Human | Breast | IDC | 3.52e-11 | -2.35e-01 | 0.1517 |
| 515 | ATP5F1 | GSM4909298 | Human | Breast | IDC | 3.80e-09 | -2.35e-01 | 0.1551 |
| 515 | ATP5F1 | GSM4909299 | Human | Breast | IDC | 1.75e-09 | -2.35e-01 | 0.035 |
| 515 | ATP5F1 | GSM4909300 | Human | Breast | IDC | 5.31e-03 | -2.35e-01 | 0.0334 |
| 515 | ATP5F1 | GSM4909301 | Human | Breast | IDC | 8.04e-10 | -2.35e-01 | 0.1577 |
| 515 | ATP5F1 | GSM4909302 | Human | Breast | IDC | 7.78e-10 | -2.35e-01 | 0.1545 |
| 515 | ATP5F1 | GSM4909304 | Human | Breast | IDC | 3.80e-09 | -2.35e-01 | 0.1636 |
| 515 | ATP5F1 | GSM4909305 | Human | Breast | IDC | 2.16e-06 | -2.35e-01 | 0.0436 |
| 515 | ATP5F1 | GSM4909306 | Human | Breast | IDC | 1.69e-10 | -2.35e-01 | 0.1564 |
| 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 | ||
| 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:000906020 | Esophagus | HGIN | aerobic respiration | 81/2587 | 189/18723 | 1.07e-22 | 9.26e-20 | 81 |
| GO:004603427 | Esophagus | HGIN | ATP metabolic process | 101/2587 | 277/18723 | 1.53e-21 | 1.02e-18 | 101 |
| GO:000609120 | Esophagus | HGIN | generation of precursor metabolites and energy | 145/2587 | 490/18723 | 3.41e-20 | 2.04e-17 | 145 |
| GO:004533320 | Esophagus | HGIN | cellular respiration | 86/2587 | 230/18723 | 2.41e-19 | 1.20e-16 | 86 |
| GO:001598020 | Esophagus | HGIN | energy derivation by oxidation of organic compounds | 105/2587 | 318/18723 | 1.16e-18 | 4.99e-16 | 105 |
| GO:000683920 | Esophagus | HGIN | mitochondrial transport | 74/2587 | 254/18723 | 1.32e-10 | 1.32e-08 | 74 |
| GO:000914419 | Esophagus | HGIN | purine nucleoside triphosphate metabolic process | 36/2587 | 88/18723 | 3.49e-10 | 3.05e-08 | 36 |
| GO:000914518 | Esophagus | HGIN | purine nucleoside triphosphate biosynthetic process | 31/2587 | 69/18723 | 3.51e-10 | 3.05e-08 | 31 |
| GO:000920618 | Esophagus | HGIN | purine ribonucleoside triphosphate biosynthetic process | 30/2587 | 68/18723 | 1.16e-09 | 9.27e-08 | 30 |
| GO:000920518 | Esophagus | HGIN | purine ribonucleoside triphosphate metabolic process | 33/2587 | 82/18723 | 3.10e-09 | 2.27e-07 | 33 |
| GO:000675417 | Esophagus | HGIN | ATP biosynthetic process | 26/2587 | 57/18723 | 6.19e-09 | 4.04e-07 | 26 |
| GO:000920117 | Esophagus | HGIN | ribonucleoside triphosphate biosynthetic process | 30/2587 | 74/18723 | 1.30e-08 | 8.15e-07 | 30 |
| GO:000914120 | Esophagus | HGIN | nucleoside triphosphate metabolic process | 39/2587 | 112/18723 | 1.56e-08 | 9.53e-07 | 39 |
| GO:001598517 | Esophagus | HGIN | energy coupled proton transport, down electrochemical gradient | 16/2587 | 26/18723 | 2.26e-08 | 1.34e-06 | 16 |
| GO:001598617 | Esophagus | HGIN | ATP synthesis coupled proton transport | 16/2587 | 26/18723 | 2.26e-08 | 1.34e-06 | 16 |
| GO:000919917 | Esophagus | HGIN | ribonucleoside triphosphate metabolic process | 33/2587 | 89/18723 | 3.42e-08 | 1.97e-06 | 33 |
| GO:000914218 | Esophagus | HGIN | nucleoside triphosphate biosynthetic process | 32/2587 | 85/18723 | 3.61e-08 | 2.04e-06 | 32 |
| GO:004277610 | Esophagus | HGIN | mitochondrial ATP synthesis coupled proton transport | 12/2587 | 19/18723 | 9.25e-07 | 3.72e-05 | 12 |
| GO:190260017 | Esophagus | HGIN | proton transmembrane transport | 43/2587 | 157/18723 | 5.51e-06 | 1.75e-04 | 43 |
| GO:000915219 | Esophagus | HGIN | purine ribonucleotide biosynthetic process | 43/2587 | 169/18723 | 3.94e-05 | 9.74e-04 | 43 |
| 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 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 |
| 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 |
| 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 |
| hsa0471419 | Breast | Precancer | Thermogenesis | 68/684 | 232/8465 | 4.40e-22 | 1.26e-20 | 9.69e-21 | 68 |
| hsa0541519 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
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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 |
| ATP5F1 | SNV | Missense_Mutation | c.155N>T | p.Gly52Val | p.G52V | P24539 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| ATP5F1 | SNV | Missense_Mutation | c.482N>G | p.Gln161Arg | p.Q161R | P24539 | protein_coding | deleterious(0) | benign(0.184) | TCGA-AO-A03T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| ATP5F1 | insertion | Frame_Shift_Ins | novel | c.116_117insCCTGATGACAAAGAACAGTACCTGTGTGGGGAGA | p.His40LeufsTer21 | p.H40Lfs*21 | P24539 | protein_coding | TCGA-BH-A0B8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | ||
| ATP5F1 | SNV | Missense_Mutation | novel | c.109G>T | p.Gly37Trp | p.G37W | P24539 | protein_coding | deleterious(0.01) | possibly_damaging(0.604) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| ATP5F1 | SNV | Missense_Mutation | c.373N>A | p.Asp125Asn | p.D125N | P24539 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR | |
| ATP5F1 | SNV | Missense_Mutation | c.618G>A | p.Met206Ile | p.M206I | P24539 | protein_coding | tolerated(0.41) | benign(0.049) | TCGA-DS-A0VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| ATP5F1 | SNV | Missense_Mutation | novel | c.385N>A | p.Glu129Lys | p.E129K | P24539 | protein_coding | deleterious(0.01) | benign(0.171) | TCGA-HM-A4S6-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |
| ATP5F1 | SNV | Missense_Mutation | rs770948319 | c.406G>A | p.Glu136Lys | p.E136K | P24539 | protein_coding | tolerated(0.52) | possibly_damaging(0.564) | TCGA-MU-A51Y-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| ATP5F1 | SNV | Missense_Mutation | c.582G>T | p.Lys194Asn | p.K194N | P24539 | protein_coding | deleterious(0.02) | probably_damaging(0.989) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| ATP5F1 | SNV | Missense_Mutation | c.189N>A | p.Phe63Leu | p.F63L | P24539 | protein_coding | tolerated(0.24) | benign(0.027) | TCGA-CA-6718-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
| Page: 1 2 3 |
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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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