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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:00486381 | Colorectum | MSS | regulation of developmental growth | 84/3467 | 330/18723 | 1.01e-03 | 1.01e-02 | 84 |
| GO:00486391 | Colorectum | MSS | positive regulation of developmental growth | 49/3467 | 174/18723 | 1.17e-03 | 1.13e-02 | 49 |
| GO:00459272 | Colorectum | MSS | positive regulation of growth | 68/3467 | 259/18723 | 1.24e-03 | 1.19e-02 | 68 |
| GO:00303072 | Colorectum | MSS | positive regulation of cell growth | 47/3467 | 166/18723 | 1.29e-03 | 1.23e-02 | 47 |
| GO:00083611 | Colorectum | MSS | regulation of cell size | 50/3467 | 181/18723 | 1.65e-03 | 1.49e-02 | 50 |
| GO:00485881 | Colorectum | MSS | developmental cell growth | 61/3467 | 234/18723 | 2.56e-03 | 2.03e-02 | 61 |
| GO:00605601 | Colorectum | MSS | developmental growth involved in morphogenesis | 61/3467 | 234/18723 | 2.56e-03 | 2.03e-02 | 61 |
| GO:00507701 | Colorectum | MSS | regulation of axonogenesis | 43/3467 | 154/18723 | 2.69e-03 | 2.12e-02 | 43 |
| GO:00109771 | Colorectum | MSS | negative regulation of neuron projection development | 39/3467 | 137/18723 | 2.86e-03 | 2.22e-02 | 39 |
| GO:00486751 | Colorectum | MSS | axon extension | 35/3467 | 120/18723 | 2.95e-03 | 2.28e-02 | 35 |
| GO:00305161 | Colorectum | MSS | regulation of axon extension | 29/3467 | 95/18723 | 3.13e-03 | 2.38e-02 | 29 |
| GO:20001142 | Colorectum | MSS | regulation of establishment of cell polarity | 10/3467 | 22/18723 | 3.42e-03 | 2.56e-02 | 10 |
| GO:0050768 | Colorectum | MSS | negative regulation of neurogenesis | 39/3467 | 140/18723 | 4.30e-03 | 3.07e-02 | 39 |
| GO:0051961 | Colorectum | MSS | negative regulation of nervous system development | 40/3467 | 145/18723 | 4.66e-03 | 3.27e-02 | 40 |
| GO:0050769 | Colorectum | MSS | positive regulation of neurogenesis | 57/3467 | 225/18723 | 6.60e-03 | 4.38e-02 | 57 |
| GO:0051960 | Colorectum | MSS | regulation of nervous system development | 103/3467 | 443/18723 | 6.68e-03 | 4.38e-02 | 103 |
| GO:1990138 | Colorectum | MSS | neuron projection extension | 45/3467 | 172/18723 | 8.06e-03 | 4.91e-02 | 45 |
| GO:00070154 | Colorectum | FAP | actin filament organization | 125/2622 | 442/18723 | 1.97e-15 | 3.03e-12 | 125 |
| GO:00325353 | Colorectum | FAP | regulation of cellular component size | 99/2622 | 383/18723 | 4.53e-10 | 1.16e-07 | 99 |
| GO:00071633 | Colorectum | FAP | establishment or maintenance of cell polarity | 64/2622 | 218/18723 | 2.83e-09 | 5.07e-07 | 64 |
| 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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