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Gene: RBFOX1 |
Gene summary for RBFOX1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RBFOX1 | Gene ID | 54715 |
| Gene name | RNA binding fox-1 homolog 1 | |
| Gene Alias | 2BP1 | |
| Cytomap | 16p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | Q59HD3 |
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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 |
| 54715 | RBFOX1 | HTA11_3410_2000001011 | Human | Colorectum | AD | 8.62e-59 | -1.25e+00 | 0.0155 |
| 54715 | RBFOX1 | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.03e-36 | -1.25e+00 | -0.1808 |
| 54715 | RBFOX1 | HTA11_2951_2000001011 | Human | Colorectum | AD | 5.14e-13 | -1.35e+00 | 0.0216 |
| 54715 | RBFOX1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 3.58e-36 | -1.44e+00 | -0.0811 |
| 54715 | RBFOX1 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.92e-13 | -7.45e-01 | -0.1088 |
| 54715 | RBFOX1 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.07e-09 | 7.09e-02 | -0.1954 |
| 54715 | RBFOX1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.24e-16 | -1.21e+00 | -0.2196 |
| 54715 | RBFOX1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.01e-37 | -1.30e+00 | -0.1207 |
| 54715 | RBFOX1 | HTA11_83_2000001011 | Human | Colorectum | SER | 4.94e-17 | -9.33e-01 | -0.1526 |
| 54715 | RBFOX1 | HTA11_696_2000001011 | Human | Colorectum | AD | 3.13e-27 | -8.16e-01 | -0.1464 |
| 54715 | RBFOX1 | HTA11_866_2000001011 | Human | Colorectum | AD | 3.51e-27 | -8.60e-01 | -0.1001 |
| 54715 | RBFOX1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.63e-25 | -9.41e-01 | -0.059 |
| 54715 | RBFOX1 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.37e-08 | -9.92e-01 | -0.1706 |
| 54715 | RBFOX1 | HTA11_5212_2000001011 | Human | Colorectum | AD | 4.39e-20 | -1.21e+00 | -0.2061 |
| 54715 | RBFOX1 | HTA11_5216_2000001011 | Human | Colorectum | SER | 4.24e-18 | -1.38e+00 | -0.1462 |
| 54715 | RBFOX1 | HTA11_546_2000001011 | Human | Colorectum | AD | 9.30e-07 | -4.01e-01 | -0.0842 |
| 54715 | RBFOX1 | HTA11_7862_2000001011 | Human | Colorectum | AD | 3.31e-12 | -9.09e-01 | -0.0179 |
| 54715 | RBFOX1 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.71e-54 | -1.31e+00 | 0.096 |
| 54715 | RBFOX1 | HTA11_4255_2000001011 | Human | Colorectum | SER | 7.18e-10 | -9.63e-01 | 0.0446 |
| 54715 | RBFOX1 | HTA11_9408_2000001011 | Human | Colorectum | AD | 2.18e-11 | -1.27e+00 | 0.0451 |
| Page: 1 2 3 4 |
| 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 |
| ∗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:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
| GO:0000377 | Colorectum | AD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000398 | Colorectum | AD | mRNA splicing, via spliceosome | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000375 | Colorectum | AD | RNA splicing, via transesterification reactions | 131/3918 | 324/18723 | 7.11e-16 | 2.22e-13 | 131 |
| GO:1903311 | Colorectum | AD | regulation of mRNA metabolic process | 117/3918 | 288/18723 | 1.69e-14 | 4.23e-12 | 117 |
| GO:0043484 | Colorectum | AD | regulation of RNA splicing | 70/3918 | 148/18723 | 6.47e-13 | 1.16e-10 | 70 |
| GO:0048024 | Colorectum | AD | regulation of mRNA splicing, via spliceosome | 50/3918 | 101/18723 | 1.62e-10 | 1.56e-08 | 50 |
| GO:0050684 | Colorectum | AD | regulation of mRNA processing | 61/3918 | 137/18723 | 4.23e-10 | 3.58e-08 | 61 |
| GO:0006403 | Colorectum | AD | RNA localization | 71/3918 | 201/18723 | 1.54e-06 | 4.76e-05 | 71 |
| GO:0000380 | Colorectum | AD | alternative mRNA splicing, via spliceosome | 33/3918 | 77/18723 | 1.13e-05 | 2.55e-04 | 33 |
| GO:0051236 | Colorectum | AD | establishment of RNA localization | 58/3918 | 166/18723 | 1.95e-05 | 4.01e-04 | 58 |
| GO:0015931 | Colorectum | AD | nucleobase-containing compound transport | 73/3918 | 222/18723 | 2.02e-05 | 4.10e-04 | 73 |
| GO:0050657 | Colorectum | AD | nucleic acid transport | 57/3918 | 163/18723 | 2.22e-05 | 4.39e-04 | 57 |
| GO:0050658 | Colorectum | AD | RNA transport | 57/3918 | 163/18723 | 2.22e-05 | 4.39e-04 | 57 |
| GO:0000381 | Colorectum | AD | regulation of alternative mRNA splicing, via spliceosome | 27/3918 | 60/18723 | 2.41e-05 | 4.66e-04 | 27 |
| GO:00083801 | Colorectum | SER | RNA splicing | 123/2897 | 434/18723 | 3.84e-12 | 8.41e-10 | 123 |
| GO:00003751 | Colorectum | SER | RNA splicing, via transesterification reactions | 90/2897 | 324/18723 | 8.68e-09 | 7.50e-07 | 90 |
| GO:00003771 | Colorectum | SER | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 89/2897 | 320/18723 | 9.82e-09 | 8.14e-07 | 89 |
| GO:00003981 | Colorectum | SER | mRNA splicing, via spliceosome | 89/2897 | 320/18723 | 9.82e-09 | 8.14e-07 | 89 |
| GO:00434841 | Colorectum | SER | regulation of RNA splicing | 49/2897 | 148/18723 | 7.02e-08 | 4.49e-06 | 49 |
| Page: 1 2 3 4 5 |
| 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 |
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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 |
| RBFOX1 | SNV | Missense_Mutation | c.587N>A | p.Arg196Gln | p.R196Q | protein_coding | deleterious(0.01) | possibly_damaging(0.834) | TCGA-A2-A0SY-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | arimidex | SD | ||
| RBFOX1 | SNV | Missense_Mutation | rs772938189 | c.481N>T | p.Arg161Trp | p.R161W | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-AO-A03O-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | doxorubicin | SD | |
| RBFOX1 | SNV | Missense_Mutation | c.196C>A | p.Gln66Lys | p.Q66K | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.53) | TCGA-BH-A18J-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | ||
| RBFOX1 | SNV | Missense_Mutation | c.739N>T | p.Pro247Ser | p.P247S | protein_coding | deleterious(0) | benign(0.082) | TCGA-D8-A145-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
| RBFOX1 | SNV | Missense_Mutation | c.664A>G | p.Thr222Ala | p.T222A | protein_coding | deleterious(0) | possibly_damaging(0.593) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | ||
| RBFOX1 | SNV | Missense_Mutation | novel | c.326A>C | p.Tyr109Ser | p.Y109S | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.554) | TCGA-D8-A27E-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen+anastrazolum | SD | |
| RBFOX1 | SNV | Missense_Mutation | c.610G>A | p.Val204Ile | p.V204I | protein_coding | deleterious(0.01) | possibly_damaging(0.844) | TCGA-E2-A154-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| RBFOX1 | SNV | Missense_Mutation | rs758592429 | c.156G>T | p.Arg52Ser | p.R52S | protein_coding | deleterious_low_confidence(0) | benign(0.01) | TCGA-E2-A1BC-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD | |
| RBFOX1 | insertion | Frame_Shift_Ins | novel | c.1181_1182insAGAGGGTATTTTAATT | p.Tyr395GlufsTer25 | p.Y395Efs*25 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |||
| RBFOX1 | SNV | Missense_Mutation | c.610G>A | p.Val204Ile | p.V204I | protein_coding | deleterious(0.01) | possibly_damaging(0.844) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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 |
| 54715 | RBFOX1 | NA | antineoplastic agents | 25823661 |
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