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Gene: F5 |
Gene summary for F5 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | F5 | Gene ID | 2153 |
| Gene name | coagulation factor V | |
| Gene Alias | FVL | |
| Cytomap | 1q24.2 | |
| Gene Type | protein-coding | GO ID | GO:0003008 | UniProtAcc | P12259 |
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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 |
| 2153 | F5 | NAFLD1 | Human | Liver | NAFLD | 2.36e-14 | 1.30e+00 | -0.04 |
| 2153 | F5 | S43 | Human | Liver | Cirrhotic | 7.16e-06 | 1.41e-01 | -0.0187 |
| 2153 | F5 | HCC1_Meng | Human | Liver | HCC | 5.06e-97 | -7.26e-02 | 0.0246 |
| 2153 | F5 | HCC2_Meng | Human | Liver | HCC | 1.66e-27 | -1.89e-01 | 0.0107 |
| 2153 | F5 | cirrhotic1 | Human | Liver | Cirrhotic | 4.04e-09 | -3.08e-01 | 0.0202 |
| 2153 | F5 | cirrhotic2 | Human | Liver | Cirrhotic | 3.27e-10 | -2.70e-01 | 0.0201 |
| 2153 | F5 | cirrhotic3 | Human | Liver | Cirrhotic | 2.56e-07 | -1.14e-01 | 0.0215 |
| 2153 | F5 | HCC1 | Human | Liver | HCC | 1.21e-34 | 6.43e+00 | 0.5336 |
| 2153 | F5 | HCC2 | Human | Liver | HCC | 4.56e-34 | 4.38e+00 | 0.5341 |
| 2153 | F5 | HCC5 | Human | Liver | HCC | 7.21e-04 | 3.72e+00 | 0.4932 |
| 2153 | F5 | Pt13.a | Human | Liver | HCC | 5.64e-06 | -1.36e-01 | 0.021 |
| 2153 | F5 | Pt13.b | Human | Liver | HCC | 1.32e-06 | -1.78e-01 | 0.0251 |
| 2153 | F5 | Pt14.a | Human | Liver | HCC | 4.03e-06 | 7.07e-02 | 0.0169 |
| 2153 | F5 | Pt14.b | Human | Liver | HCC | 2.04e-02 | 6.43e-02 | 0.018 |
| 2153 | F5 | Pt14.d | Human | Liver | HCC | 3.40e-06 | -7.53e-02 | 0.0143 |
| 2153 | F5 | S014 | Human | Liver | HCC | 1.60e-20 | 1.49e+00 | 0.2254 |
| 2153 | F5 | S015 | Human | Liver | HCC | 1.05e-15 | 1.38e+00 | 0.2375 |
| 2153 | F5 | S016 | Human | Liver | HCC | 5.00e-19 | 1.25e+00 | 0.2243 |
| 2153 | F5 | S027 | Human | Liver | HCC | 1.52e-11 | 1.18e+00 | 0.2446 |
| 2153 | F5 | S028 | Human | Liver | HCC | 1.29e-25 | 1.29e+00 | 0.2503 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:00021819 | Breast | Precancer | cytoplasmic translation | 80/1080 | 148/18723 | 1.59e-59 | 8.54e-56 | 80 |
| GO:00226139 | Breast | Precancer | ribonucleoprotein complex biogenesis | 79/1080 | 463/18723 | 2.11e-18 | 1.03e-15 | 79 |
| GO:00971939 | Breast | Precancer | intrinsic apoptotic signaling pathway | 59/1080 | 288/18723 | 8.07e-18 | 3.60e-15 | 59 |
| GO:20012339 | Breast | Precancer | regulation of apoptotic signaling pathway | 65/1080 | 356/18723 | 7.70e-17 | 3.17e-14 | 65 |
| GO:20012429 | Breast | Precancer | regulation of intrinsic apoptotic signaling pathway | 41/1080 | 164/18723 | 6.48e-16 | 2.31e-13 | 41 |
| GO:00718269 | Breast | Precancer | ribonucleoprotein complex subunit organization | 48/1080 | 227/18723 | 2.68e-15 | 8.45e-13 | 48 |
| GO:00226189 | Breast | Precancer | ribonucleoprotein complex assembly | 47/1080 | 220/18723 | 3.47e-15 | 1.03e-12 | 47 |
| GO:00083809 | Breast | Precancer | RNA splicing | 65/1080 | 434/18723 | 1.27e-12 | 2.53e-10 | 65 |
| GO:00434849 | Breast | Precancer | regulation of RNA splicing | 34/1080 | 148/18723 | 2.66e-12 | 4.75e-10 | 34 |
| GO:00064138 | Breast | Precancer | translational initiation | 30/1080 | 118/18723 | 3.23e-12 | 5.58e-10 | 30 |
| GO:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
| GO:00457279 | Breast | Precancer | positive regulation of translation | 32/1080 | 136/18723 | 5.89e-12 | 9.27e-10 | 32 |
| GO:00003759 | Breast | Precancer | RNA splicing, via transesterification reactions | 52/1080 | 324/18723 | 1.74e-11 | 2.22e-09 | 52 |
| GO:00003779 | Breast | Precancer | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:00003989 | Breast | Precancer | mRNA splicing, via spliceosome | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:00342509 | Breast | Precancer | positive regulation of cellular amide metabolic process | 33/1080 | 162/18723 | 1.72e-10 | 1.77e-08 | 33 |
| GO:20012445 | Breast | Precancer | positive regulation of intrinsic apoptotic signaling pathway | 17/1080 | 58/18723 | 1.59e-08 | 1.12e-06 | 17 |
| GO:00064466 | Breast | Precancer | regulation of translational initiation | 19/1080 | 79/18723 | 7.99e-08 | 4.60e-06 | 19 |
| GO:20012356 | Breast | Precancer | positive regulation of apoptotic signaling pathway | 24/1080 | 126/18723 | 1.98e-07 | 1.01e-05 | 24 |
| GO:19017989 | Breast | Precancer | positive regulation of signal transduction by p53 class mediator | 10/1080 | 25/18723 | 5.77e-07 | 2.49e-05 | 10 |
| 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 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160 161 162 163 164 165 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa04610 | Liver | NAFLD | Complement and coagulation cascades | 35/1043 | 86/8465 | 2.48e-11 | 2.04e-09 | 1.64e-09 | 35 |
| hsa046101 | Liver | NAFLD | Complement and coagulation cascades | 35/1043 | 86/8465 | 2.48e-11 | 2.04e-09 | 1.64e-09 | 35 |
| hsa046102 | Liver | Cirrhotic | Complement and coagulation cascades | 48/2530 | 86/8465 | 4.41e-07 | 5.44e-06 | 3.35e-06 | 48 |
| hsa046103 | Liver | Cirrhotic | Complement and coagulation cascades | 48/2530 | 86/8465 | 4.41e-07 | 5.44e-06 | 3.35e-06 | 48 |
| hsa046104 | Liver | HCC | Complement and coagulation cascades | 57/4020 | 86/8465 | 3.19e-04 | 1.45e-03 | 8.04e-04 | 57 |
| hsa046105 | Liver | HCC | Complement and coagulation cascades | 57/4020 | 86/8465 | 3.19e-04 | 1.45e-03 | 8.04e-04 | 57 |
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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 |
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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. |
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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 |
| F5 | SNV | Missense_Mutation | novel | c.4241N>T | p.Asp1414Val | p.D1414V | P12259 | protein_coding | deleterious_low_confidence(0.04) | benign(0.209) | TCGA-A2-A4RW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| F5 | SNV | Missense_Mutation | novel | c.3913N>G | p.Pro1305Ala | p.P1305A | P12259 | protein_coding | deleterious_low_confidence(0.03) | benign(0.265) | TCGA-A2-A4RW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| F5 | SNV | Missense_Mutation | novel | c.1495C>A | p.Gln499Lys | p.Q499K | P12259 | protein_coding | deleterious(0.02) | possibly_damaging(0.541) | TCGA-A7-A0DB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| F5 | SNV | Missense_Mutation | c.6397N>T | p.Ile2133Leu | p.I2133L | P12259 | protein_coding | deleterious(0.02) | possibly_damaging(0.622) | TCGA-A8-A06Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| F5 | SNV | Missense_Mutation | c.6396N>T | p.Lys2132Asn | p.K2132N | P12259 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-A8-A07L-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | CR | ||
| F5 | SNV | Missense_Mutation | novel | c.4087N>A | p.His1363Asn | p.H1363N | P12259 | protein_coding | tolerated_low_confidence(0.14) | benign(0.023) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| F5 | SNV | Missense_Mutation | novel | c.4086N>A | p.Ser1362Arg | p.S1362R | P12259 | protein_coding | tolerated_low_confidence(0.09) | benign(0.168) | TCGA-A8-A08R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| F5 | SNV | Missense_Mutation | c.622G>C | p.Asp208His | p.D208H | P12259 | protein_coding | tolerated(0.13) | benign(0.123) | TCGA-A8-A09G-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| F5 | SNV | Missense_Mutation | c.1447N>A | p.Tyr483Asn | p.Y483N | P12259 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A8-A09I-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
| F5 | SNV | Missense_Mutation | novel | c.5676N>C | p.Gln1892His | p.Q1892H | P12259 | protein_coding | deleterious(0.04) | probably_damaging(0.999) | TCGA-AC-A3BB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | CR |
| 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 |
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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 |
| 2153 | F5 | DRUGGABLE GENOME | drotrecogin alfa | 15118525 | ||
| 2153 | F5 | DRUGGABLE GENOME | rivaroxaban | RIVAROXABAN | ||
| 2153 | F5 | DRUGGABLE GENOME | Rivaroxaban | RIVAROXABAN | ||
| 2153 | F5 | DRUGGABLE GENOME | estrogens | ESTRONE SODIUM SULFATE | 11532625,16113779,12067913,12869355,16301339,9459317,10073976,15467059,11859850,10943572,12069454,12138364,14551147,7968118,11703344 | |
| 2153 | F5 | DRUGGABLE GENOME | Drotrecogin alfa | |||
| 2153 | F5 | DRUGGABLE GENOME | Eltrombopag | ELTROMBOPAG | ||
| 2153 | F5 | DRUGGABLE GENOME | DROTRECOGIN ALFA | |||
| 2153 | F5 | DRUGGABLE GENOME | hormonal contraceptives for systemic use | 11532625,16113779,15208046,15946211,12869355,16301339,9459317,10073976,15467059,11859850,10943572,12069454,16769590,12138364,14551147,7968118 | ||
| 2153 | F5 | DRUGGABLE GENOME | inhibitor | CHEMBL2109065 | DROTRECOGIN ALFA (ACTIVATED) | |
| 2153 | F5 | DRUGGABLE GENOME | THROMBIN | THROMBIN |
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