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Gene: SF3B4 |
Gene summary for SF3B4 |
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Gene information | Species | Human | Gene symbol | SF3B4 | Gene ID | 10262 |
Gene name | splicing factor 3b subunit 4 | |
Gene Alias | AFD1 | |
Cytomap | 1q21.2 | |
Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | B3KUJ0 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
10262 | SF3B4 | SYSMH2 | Human | Oral cavity | OSCC | 1.72e-21 | 6.98e-01 | 0.2326 |
10262 | SF3B4 | SYSMH3 | Human | Oral cavity | OSCC | 1.92e-25 | 6.73e-01 | 0.2442 |
10262 | SF3B4 | SYSMH4 | Human | Oral cavity | OSCC | 2.03e-02 | 1.51e-01 | 0.1226 |
10262 | SF3B4 | SYSMH5 | Human | Oral cavity | OSCC | 5.09e-11 | 4.32e-01 | 0.0647 |
10262 | SF3B4 | SYSMH6 | Human | Oral cavity | OSCC | 1.67e-05 | 2.57e-01 | 0.1275 |
10262 | SF3B4 | P4_S8_cSCC | Human | Skin | cSCC | 3.73e-02 | 8.16e-02 | -0.3095 |
10262 | SF3B4 | P1_cSCC | Human | Skin | cSCC | 8.70e-18 | 7.75e-01 | 0.0292 |
10262 | SF3B4 | P2_cSCC | Human | Skin | cSCC | 6.70e-12 | 4.98e-01 | -0.024 |
10262 | SF3B4 | P4_cSCC | Human | Skin | cSCC | 2.44e-14 | 6.47e-01 | -0.00290000000000005 |
10262 | SF3B4 | P10_cSCC | Human | Skin | cSCC | 4.68e-22 | 7.11e-01 | 0.1017 |
10262 | SF3B4 | cSCC_p7 | Human | Skin | cSCC | 1.82e-03 | -9.09e-02 | -0.2332 |
10262 | SF3B4 | male-WTA | Human | Thyroid | PTC | 1.16e-40 | 3.59e-01 | 0.1037 |
10262 | SF3B4 | PTC01 | Human | Thyroid | PTC | 3.90e-07 | 2.79e-02 | 0.1899 |
10262 | SF3B4 | PTC03 | Human | Thyroid | PTC | 1.45e-03 | 3.65e-02 | 0.1784 |
10262 | SF3B4 | PTC04 | Human | Thyroid | PTC | 1.83e-15 | 2.91e-02 | 0.1927 |
10262 | SF3B4 | PTC05 | Human | Thyroid | PTC | 7.18e-14 | 4.69e-01 | 0.2065 |
10262 | SF3B4 | PTC06 | Human | Thyroid | PTC | 4.26e-22 | 3.93e-01 | 0.2057 |
10262 | SF3B4 | PTC07 | Human | Thyroid | PTC | 3.33e-26 | 2.42e-01 | 0.2044 |
10262 | SF3B4 | ATC09 | Human | Thyroid | ATC | 1.30e-03 | 2.35e-02 | 0.2871 |
10262 | SF3B4 | ATC11 | Human | Thyroid | ATC | 9.99e-03 | 2.25e-01 | 0.3386 |
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∗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 |
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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). |
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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:1903313 | Colorectum | AD | positive regulation of mRNA metabolic process | 44/3918 | 118/18723 | 3.20e-05 | 5.87e-04 | 44 |
GO:0033120 | Colorectum | AD | positive regulation of RNA splicing | 19/3918 | 37/18723 | 4.08e-05 | 7.26e-04 | 19 |
GO:0048026 | Colorectum | AD | positive regulation of mRNA splicing, via spliceosome | 12/3918 | 22/18723 | 5.38e-04 | 5.74e-03 | 12 |
GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
GO:0000375111 | Esophagus | ESCC | RNA splicing, via transesterification reactions | 248/8552 | 324/18723 | 3.05e-30 | 1.49e-27 | 248 |
GO:0000377111 | Esophagus | ESCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
GO:0000398111 | Esophagus | ESCC | mRNA splicing, via spliceosome | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
GO:1903311110 | Esophagus | ESCC | regulation of mRNA metabolic process | 210/8552 | 288/18723 | 3.25e-21 | 5.56e-19 | 210 |
GO:0043484111 | Esophagus | ESCC | regulation of RNA splicing | 116/8552 | 148/18723 | 3.18e-16 | 2.38e-14 | 116 |
GO:0050684110 | Esophagus | ESCC | regulation of mRNA processing | 109/8552 | 137/18723 | 3.51e-16 | 2.59e-14 | 109 |
GO:0048024111 | Esophagus | ESCC | regulation of mRNA splicing, via spliceosome | 78/8552 | 101/18723 | 8.72e-11 | 2.66e-09 | 78 |
GO:190331316 | Esophagus | ESCC | positive regulation of mRNA metabolic process | 87/8552 | 118/18723 | 5.10e-10 | 1.32e-08 | 87 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
SF3B4 | SNV | Missense_Mutation | c.1061G>T | p.Arg354Leu | p.R354L | Q15427 | protein_coding | deleterious(0.01) | benign(0.048) | TCGA-A2-A0CW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
SF3B4 | SNV | Missense_Mutation | c.360N>G | p.Phe120Leu | p.F120L | Q15427 | protein_coding | deleterious(0.03) | probably_damaging(0.998) | TCGA-C8-A12P-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SF3B4 | insertion | Frame_Shift_Ins | rs782357237 | c.1060dupC | p.Arg354ProfsTer132 | p.R354Pfs*132 | Q15427 | protein_coding | TCGA-D8-A13Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
SF3B4 | SNV | Missense_Mutation | novel | c.718N>T | p.Pro240Ser | p.P240S | Q15427 | protein_coding | tolerated(0.19) | benign(0.009) | TCGA-HM-A6W2-06 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
SF3B4 | SNV | Missense_Mutation | c.869A>G | p.His290Arg | p.H290R | Q15427 | protein_coding | tolerated(0.3) | benign(0.007) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SF3B4 | SNV | Missense_Mutation | novel | c.1249N>A | p.Pro417Thr | p.P417T | Q15427 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.981) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SF3B4 | SNV | Missense_Mutation | novel | c.1259G>A | p.Gly420Asp | p.G420D | Q15427 | protein_coding | deleterious_low_confidence(0) | benign(0.029) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
SF3B4 | SNV | Missense_Mutation | c.578G>A | p.Arg193Gln | p.R193Q | Q15427 | protein_coding | deleterious(0.05) | probably_damaging(0.95) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
SF3B4 | SNV | Missense_Mutation | c.1120N>T | p.Arg374Cys | p.R374C | Q15427 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.725) | TCGA-D5-6540-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SF3B4 | SNV | Missense_Mutation | c.940N>T | p.His314Tyr | p.H314Y | Q15427 | protein_coding | deleterious(0) | benign(0.066) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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