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Gene: RUFY3 |
Gene summary for RUFY3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RUFY3 | Gene ID | 22902 |
| Gene name | RUN and FYVE domain containing 3 | |
| Gene Alias | RIPX | |
| Cytomap | 4q13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q7L099 |
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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 |
| 22902 | RUFY3 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.08e-03 | -3.14e-01 | 0.294 |
| 22902 | RUFY3 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 9.98e-06 | -3.53e-01 | 0.3005 |
| 22902 | RUFY3 | A015-C-203 | Human | Colorectum | FAP | 6.31e-20 | -2.94e-01 | -0.1294 |
| 22902 | RUFY3 | A015-C-204 | Human | Colorectum | FAP | 3.20e-04 | -3.30e-01 | -0.0228 |
| 22902 | RUFY3 | A014-C-040 | Human | Colorectum | FAP | 2.93e-04 | -5.25e-01 | -0.1184 |
| 22902 | RUFY3 | A002-C-201 | Human | Colorectum | FAP | 5.83e-10 | -3.09e-01 | 0.0324 |
| 22902 | RUFY3 | A001-C-119 | Human | Colorectum | FAP | 6.55e-03 | -2.96e-01 | -0.1557 |
| 22902 | RUFY3 | A001-C-108 | Human | Colorectum | FAP | 3.99e-08 | -1.76e-01 | -0.0272 |
| 22902 | RUFY3 | A002-C-205 | Human | Colorectum | FAP | 2.37e-15 | -2.11e-01 | -0.1236 |
| 22902 | RUFY3 | A015-C-006 | Human | Colorectum | FAP | 3.74e-12 | -3.86e-01 | -0.0994 |
| 22902 | RUFY3 | A015-C-106 | Human | Colorectum | FAP | 3.95e-09 | -2.47e-01 | -0.0511 |
| 22902 | RUFY3 | A002-C-114 | Human | Colorectum | FAP | 5.28e-12 | -2.81e-01 | -0.1561 |
| 22902 | RUFY3 | A015-C-104 | Human | Colorectum | FAP | 1.72e-17 | -3.08e-01 | -0.1899 |
| 22902 | RUFY3 | A001-C-014 | Human | Colorectum | FAP | 5.27e-11 | -2.80e-01 | 0.0135 |
| 22902 | RUFY3 | A002-C-016 | Human | Colorectum | FAP | 6.88e-14 | -3.01e-01 | 0.0521 |
| 22902 | RUFY3 | A015-C-002 | Human | Colorectum | FAP | 2.49e-07 | -3.54e-01 | -0.0763 |
| 22902 | RUFY3 | A001-C-203 | Human | Colorectum | FAP | 5.71e-07 | -2.03e-01 | -0.0481 |
| 22902 | RUFY3 | A002-C-116 | Human | Colorectum | FAP | 9.48e-21 | -2.68e-01 | -0.0452 |
| 22902 | RUFY3 | A014-C-008 | Human | Colorectum | FAP | 3.03e-11 | -4.31e-01 | -0.191 |
| 22902 | RUFY3 | A018-E-020 | Human | Colorectum | FAP | 7.97e-13 | -2.73e-01 | -0.2034 |
| 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 | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:005122222 | Liver | HCC | positive regulation of protein transport | 194/7958 | 303/18723 | 2.41e-14 | 1.56e-12 | 194 |
| GO:000701522 | Liver | HCC | actin filament organization | 252/7958 | 442/18723 | 3.83e-10 | 1.25e-08 | 252 |
| GO:001604921 | Liver | HCC | cell growth | 269/7958 | 482/18723 | 1.84e-09 | 5.35e-08 | 269 |
| GO:003253522 | Liver | HCC | regulation of cellular component size | 217/7958 | 383/18723 | 1.28e-08 | 3.14e-07 | 217 |
| GO:000716322 | Liver | HCC | establishment or maintenance of cell polarity | 133/7958 | 218/18723 | 2.48e-08 | 5.73e-07 | 133 |
| GO:000155821 | Liver | HCC | regulation of cell growth | 228/7958 | 414/18723 | 1.34e-07 | 2.55e-06 | 228 |
| GO:003134611 | Liver | HCC | positive regulation of cell projection organization | 193/7958 | 353/18723 | 2.28e-06 | 3.08e-05 | 193 |
| GO:003001022 | Liver | HCC | establishment of cell polarity | 82/7958 | 143/18723 | 2.38e-04 | 1.79e-03 | 82 |
| GO:001072011 | Liver | HCC | positive regulation of cell development | 155/7958 | 298/18723 | 5.39e-04 | 3.48e-03 | 155 |
| GO:006056011 | Liver | HCC | developmental growth involved in morphogenesis | 124/7958 | 234/18723 | 7.37e-04 | 4.47e-03 | 124 |
| GO:001097511 | Liver | HCC | regulation of neuron projection development | 220/7958 | 445/18723 | 1.68e-03 | 8.78e-03 | 220 |
| GO:004867511 | Liver | HCC | axon extension | 67/7958 | 120/18723 | 2.17e-03 | 1.09e-02 | 67 |
| GO:199013811 | Liver | HCC | neuron projection extension | 92/7958 | 172/18723 | 2.31e-03 | 1.14e-02 | 92 |
| GO:004858811 | Liver | HCC | developmental cell growth | 121/7958 | 234/18723 | 2.68e-03 | 1.28e-02 | 121 |
| GO:00507674 | Liver | HCC | regulation of neurogenesis | 181/7958 | 364/18723 | 3.00e-03 | 1.40e-02 | 181 |
| GO:004577321 | Liver | HCC | positive regulation of axon extension | 27/7958 | 42/18723 | 3.60e-03 | 1.60e-02 | 27 |
| GO:00507693 | Liver | HCC | positive regulation of neurogenesis | 116/7958 | 225/18723 | 3.67e-03 | 1.63e-02 | 116 |
| GO:003030711 | Liver | HCC | positive regulation of cell growth | 88/7958 | 166/18723 | 3.95e-03 | 1.74e-02 | 88 |
| GO:00083614 | Liver | HCC | regulation of cell size | 95/7958 | 181/18723 | 4.15e-03 | 1.81e-02 | 95 |
| GO:00305164 | Liver | HCC | regulation of axon extension | 52/7958 | 95/18723 | 1.07e-02 | 3.97e-02 | 52 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
| 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 |
| RUFY3 | SNV | Missense_Mutation | c.10C>G | p.Leu4Val | p.L4V | Q7L099 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.986) | TCGA-A2-A04T-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD | |
| RUFY3 | SNV | Missense_Mutation | novel | c.1408G>T | p.Asp470Tyr | p.D470Y | Q7L099 | protein_coding | deleterious(0) | possibly_damaging(0.863) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD |
| RUFY3 | SNV | Missense_Mutation | c.1309G>T | p.Ala437Ser | p.A437S | Q7L099 | protein_coding | tolerated(0.41) | benign(0.023) | TCGA-A8-A09A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| RUFY3 | SNV | Missense_Mutation | rs748059452 | c.754N>A | p.Glu252Lys | p.E252K | Q7L099 | protein_coding | tolerated(0.29) | probably_damaging(0.956) | TCGA-B6-A0IK-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| RUFY3 | SNV | Missense_Mutation | c.1065N>T | p.Leu355Phe | p.L355F | Q7L099 | protein_coding | tolerated(0.06) | probably_damaging(0.982) | TCGA-D8-A1JK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RUFY3 | SNV | Missense_Mutation | c.1078G>A | p.Glu360Lys | p.E360K | Q7L099 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EW-A1J5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| RUFY3 | SNV | Missense_Mutation | novel | c.41C>T | p.Thr14Ile | p.T14I | Q7L099 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RUFY3 | SNV | Missense_Mutation | novel | c.1095G>A | p.Met365Ile | p.M365I | Q7L099 | protein_coding | tolerated(0.18) | benign(0) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| RUFY3 | SNV | Missense_Mutation | novel | c.209N>C | p.Met70Thr | p.M70T | Q7L099 | protein_coding | tolerated(0.47) | benign(0.115) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| RUFY3 | SNV | Missense_Mutation | c.1372N>C | p.Glu458Gln | p.E458Q | Q7L099 | protein_coding | tolerated(0.06) | benign(0.027) | TCGA-EK-A3GK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 |
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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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