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Gene: SF3B3 |
Gene summary for SF3B3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SF3B3 | Gene ID | 23450 |
| Gene name | splicing factor 3b subunit 3 | |
| Gene Alias | RSE1 | |
| Cytomap | 16q22.1 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | A8K6V3 |
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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 |
| 23450 | SF3B3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.57e-05 | 5.03e-01 | -0.059 |
| 23450 | SF3B3 | HTA11_866_3004761011 | Human | Colorectum | AD | 2.94e-04 | 3.71e-01 | 0.096 |
| 23450 | SF3B3 | HTA11_6818_2000001021 | Human | Colorectum | AD | 1.21e-02 | 3.59e-01 | 0.0588 |
| 23450 | SF3B3 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.05e-04 | 4.54e-01 | 0.294 |
| 23450 | SF3B3 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 7.51e-12 | 7.74e-01 | 0.281 |
| 23450 | SF3B3 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.86e-13 | 8.38e-01 | 0.3859 |
| 23450 | SF3B3 | A015-C-203 | Human | Colorectum | FAP | 2.61e-15 | -2.55e-01 | -0.1294 |
| 23450 | SF3B3 | A015-C-204 | Human | Colorectum | FAP | 2.91e-02 | -1.69e-01 | -0.0228 |
| 23450 | SF3B3 | A002-C-201 | Human | Colorectum | FAP | 2.18e-05 | -2.02e-01 | 0.0324 |
| 23450 | SF3B3 | A001-C-108 | Human | Colorectum | FAP | 1.58e-06 | -1.34e-01 | -0.0272 |
| 23450 | SF3B3 | A002-C-205 | Human | Colorectum | FAP | 1.57e-11 | -1.80e-01 | -0.1236 |
| 23450 | SF3B3 | A015-C-006 | Human | Colorectum | FAP | 1.54e-07 | -1.70e-01 | -0.0994 |
| 23450 | SF3B3 | A015-C-106 | Human | Colorectum | FAP | 4.94e-07 | -1.33e-01 | -0.0511 |
| 23450 | SF3B3 | A002-C-114 | Human | Colorectum | FAP | 3.15e-07 | -2.26e-01 | -0.1561 |
| 23450 | SF3B3 | A015-C-104 | Human | Colorectum | FAP | 1.36e-15 | -2.25e-01 | -0.1899 |
| 23450 | SF3B3 | A001-C-014 | Human | Colorectum | FAP | 4.36e-09 | -2.06e-01 | 0.0135 |
| 23450 | SF3B3 | A002-C-016 | Human | Colorectum | FAP | 2.62e-12 | -2.70e-01 | 0.0521 |
| 23450 | SF3B3 | A015-C-002 | Human | Colorectum | FAP | 1.52e-04 | -1.82e-01 | -0.0763 |
| 23450 | SF3B3 | A001-C-203 | Human | Colorectum | FAP | 3.12e-04 | -1.20e-01 | -0.0481 |
| 23450 | SF3B3 | A002-C-116 | Human | Colorectum | FAP | 1.84e-17 | -2.13e-01 | -0.0452 |
| 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 | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| 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:0042176 | Colorectum | AD | regulation of protein catabolic process | 160/3918 | 391/18723 | 1.06e-19 | 7.34e-17 | 160 |
| 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:0009895 | Colorectum | AD | negative regulation of catabolic process | 124/3918 | 320/18723 | 1.66e-13 | 3.35e-11 | 124 |
| GO:0042177 | Colorectum | AD | negative regulation of protein catabolic process | 55/3918 | 121/18723 | 1.19e-09 | 8.85e-08 | 55 |
| GO:00083802 | Colorectum | MSS | RNA splicing | 159/3467 | 434/18723 | 1.75e-19 | 1.22e-16 | 159 |
| GO:00421762 | Colorectum | MSS | regulation of protein catabolic process | 145/3467 | 391/18723 | 2.03e-18 | 1.17e-15 | 145 |
| GO:00003772 | Colorectum | MSS | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 121/3467 | 320/18723 | 2.52e-16 | 8.27e-14 | 121 |
| GO:00003982 | Colorectum | MSS | mRNA splicing, via spliceosome | 121/3467 | 320/18723 | 2.52e-16 | 8.27e-14 | 121 |
| GO:00003752 | Colorectum | MSS | RNA splicing, via transesterification reactions | 122/3467 | 324/18723 | 2.75e-16 | 8.58e-14 | 122 |
| GO:00098952 | Colorectum | MSS | negative regulation of catabolic process | 110/3467 | 320/18723 | 7.88e-12 | 1.20e-09 | 110 |
| GO:00421772 | Colorectum | MSS | negative regulation of protein catabolic process | 47/3467 | 121/18723 | 1.28e-07 | 6.01e-06 | 47 |
| GO:00421764 | Colorectum | FAP | regulation of protein catabolic process | 106/2622 | 391/18723 | 5.00e-12 | 3.06e-09 | 106 |
| GO:00098954 | Colorectum | FAP | negative regulation of catabolic process | 91/2622 | 320/18723 | 9.66e-12 | 4.96e-09 | 91 |
| GO:00083804 | Colorectum | FAP | RNA splicing | 108/2622 | 434/18723 | 7.90e-10 | 1.86e-07 | 108 |
| GO:00003754 | Colorectum | FAP | RNA splicing, via transesterification reactions | 84/2622 | 324/18723 | 8.06e-09 | 1.10e-06 | 84 |
| GO:00003774 | Colorectum | FAP | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 83/2622 | 320/18723 | 9.66e-09 | 1.23e-06 | 83 |
| GO:00003984 | Colorectum | FAP | mRNA splicing, via spliceosome | 83/2622 | 320/18723 | 9.66e-09 | 1.23e-06 | 83 |
| Page: 1 2 3 4 5 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa03040 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
| hsa030401 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
| hsa030402 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
| hsa030403 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
| hsa0304018 | Esophagus | HGIN | Spliceosome | 79/1383 | 217/8465 | 3.22e-13 | 7.00e-12 | 5.56e-12 | 79 |
| hsa0304019 | Esophagus | HGIN | Spliceosome | 79/1383 | 217/8465 | 3.22e-13 | 7.00e-12 | 5.56e-12 | 79 |
| hsa0304027 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa0304037 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa030407 | Liver | Cirrhotic | Spliceosome | 102/2530 | 217/8465 | 5.69e-08 | 9.47e-07 | 5.84e-07 | 102 |
| hsa0304012 | Liver | Cirrhotic | Spliceosome | 102/2530 | 217/8465 | 5.69e-08 | 9.47e-07 | 5.84e-07 | 102 |
| hsa0304022 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
| hsa0304032 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
| hsa0304016 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
| hsa0304017 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
| hsa0304026 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
| hsa0304036 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
| Page: 1 |
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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 |
| SF3B3 | SNV | Missense_Mutation | novel | c.2190N>G | p.His730Gln | p.H730Q | Q15393 | protein_coding | tolerated(0.45) | benign(0.007) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SF3B3 | SNV | Missense_Mutation | novel | c.2479N>A | p.Ala827Thr | p.A827T | Q15393 | protein_coding | tolerated(0.42) | benign(0.009) | TCGA-AJ-A23O-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SF3B3 | SNV | Missense_Mutation | novel | c.1903N>T | p.Ala635Ser | p.A635S | Q15393 | protein_coding | tolerated(0.51) | benign(0.014) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
| SF3B3 | SNV | Missense_Mutation | c.1057T>C | p.Phe353Leu | p.F353L | Q15393 | protein_coding | deleterious(0.04) | benign(0.033) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SF3B3 | SNV | Missense_Mutation | c.2074N>T | p.Arg692Trp | p.R692W | Q15393 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SF3B3 | SNV | Missense_Mutation | c.3385N>A | p.Leu1129Ile | p.L1129I | Q15393 | protein_coding | deleterious(0.03) | probably_damaging(0.954) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SF3B3 | SNV | Missense_Mutation | novel | c.2780C>T | p.Thr927Ile | p.T927I | Q15393 | protein_coding | tolerated(0.4) | benign(0.009) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SF3B3 | SNV | Missense_Mutation | novel | c.788A>T | p.Asp263Val | p.D263V | Q15393 | protein_coding | deleterious(0) | benign(0.068) | TCGA-AP-A1DO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SF3B3 | SNV | Missense_Mutation | c.1057N>A | p.Phe353Ile | p.F353I | Q15393 | protein_coding | deleterious(0.01) | benign(0.314) | TCGA-AX-A05Z-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | SD | |
| SF3B3 | SNV | Missense_Mutation | rs778558010 | c.1387N>T | p.Arg463Cys | p.R463C | Q15393 | protein_coding | deleterious(0) | benign(0.244) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| 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 |
| 23450 | SF3B3 | DRUGGABLE GENOME | PLADIENOLIDE B | PLADIENOLIDE B | 17643112 | |
| 23450 | SF3B3 | DRUGGABLE GENOME | PLA D | PLA D | 17643112 |
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