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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:00092609 | Endometrium | AEH | ribonucleotide biosynthetic process | 35/2100 | 182/18723 | 9.88e-04 | 8.90e-03 | 35 |
| GO:00463909 | Endometrium | AEH | ribose phosphate biosynthetic process | 36/2100 | 190/18723 | 1.11e-03 | 9.74e-03 | 36 |
| GO:000675314 | Endometrium | AEH | nucleoside phosphate metabolic process | 78/2100 | 497/18723 | 1.34e-03 | 1.13e-02 | 78 |
| GO:00435362 | Endometrium | AEH | positive regulation of blood vessel endothelial cell migration | 18/2100 | 76/18723 | 1.55e-03 | 1.27e-02 | 18 |
| GO:00061648 | Endometrium | AEH | purine nucleotide biosynthetic process | 35/2100 | 191/18723 | 2.34e-03 | 1.76e-02 | 35 |
| GO:00435342 | Endometrium | AEH | blood vessel endothelial cell migration | 32/2100 | 176/18723 | 3.97e-03 | 2.66e-02 | 32 |
| GO:00725228 | Endometrium | AEH | purine-containing compound biosynthetic process | 35/2100 | 200/18723 | 5.05e-03 | 3.16e-02 | 35 |
| GO:0001935 | Endometrium | AEH | endothelial cell proliferation | 33/2100 | 193/18723 | 8.99e-03 | 4.87e-02 | 33 |
| GO:004603417 | Endometrium | EEC | ATP metabolic process | 107/2168 | 277/18723 | 1.32e-31 | 3.95e-28 | 107 |
| GO:000611916 | Endometrium | EEC | oxidative phosphorylation | 71/2168 | 141/18723 | 5.89e-30 | 1.18e-26 | 71 |
| GO:000906015 | Endometrium | EEC | aerobic respiration | 79/2168 | 189/18723 | 2.63e-26 | 3.95e-23 | 79 |
| GO:004533315 | Endometrium | EEC | cellular respiration | 83/2168 | 230/18723 | 1.72e-22 | 2.06e-19 | 83 |
| GO:001598015 | Endometrium | EEC | energy derivation by oxidation of organic compounds | 97/2168 | 318/18723 | 5.37e-20 | 3.58e-17 | 97 |
| GO:000609115 | Endometrium | EEC | generation of precursor metabolites and energy | 125/2168 | 490/18723 | 3.76e-18 | 1.88e-15 | 125 |
| GO:000914516 | Endometrium | EEC | purine nucleoside triphosphate biosynthetic process | 30/2168 | 69/18723 | 2.24e-11 | 3.36e-09 | 30 |
| GO:000683915 | Endometrium | EEC | mitochondrial transport | 67/2168 | 254/18723 | 5.04e-11 | 7.03e-09 | 67 |
| GO:000920616 | Endometrium | EEC | purine ribonucleoside triphosphate biosynthetic process | 29/2168 | 68/18723 | 8.54e-11 | 1.09e-08 | 29 |
| GO:001598515 | Endometrium | EEC | energy coupled proton transport, down electrochemical gradient | 17/2168 | 26/18723 | 1.27e-10 | 1.53e-08 | 17 |
| GO:001598615 | Endometrium | EEC | ATP synthesis coupled proton transport | 17/2168 | 26/18723 | 1.27e-10 | 1.53e-08 | 17 |
| GO:000914416 | Endometrium | EEC | purine nucleoside triphosphate metabolic process | 33/2168 | 88/18723 | 2.71e-10 | 2.95e-08 | 33 |
| 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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