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Gene: SF3A2 |
Gene summary for SF3A2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SF3A2 | Gene ID | 8175 |
| Gene name | splicing factor 3a subunit 2 | |
| Gene Alias | PRP11 | |
| Cytomap | 19p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | Q05DF2 |
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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 |
| 8175 | SF3A2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 4.06e-04 | 1.96e-01 | 0.0155 |
| 8175 | SF3A2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.62e-03 | 2.43e-01 | -0.059 |
| 8175 | SF3A2 | HTA11_9408_2000001011 | Human | Colorectum | AD | 4.28e-07 | 7.19e-01 | 0.0451 |
| 8175 | SF3A2 | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.88e-06 | 3.99e-01 | 0.0338 |
| 8175 | SF3A2 | HTA11_7696_3000711011 | Human | Colorectum | AD | 9.16e-16 | 6.35e-01 | 0.0674 |
| 8175 | SF3A2 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.15e-03 | 3.82e-01 | 0.2585 |
| 8175 | SF3A2 | LZE4T | Human | Esophagus | ESCC | 3.65e-19 | 4.52e-01 | 0.0811 |
| 8175 | SF3A2 | LZE7T | Human | Esophagus | ESCC | 1.52e-08 | 4.53e-01 | 0.0667 |
| 8175 | SF3A2 | LZE8T | Human | Esophagus | ESCC | 2.51e-11 | 3.08e-01 | 0.067 |
| 8175 | SF3A2 | LZE20T | Human | Esophagus | ESCC | 1.36e-13 | 4.34e-01 | 0.0662 |
| 8175 | SF3A2 | LZE22D1 | Human | Esophagus | HGIN | 6.08e-08 | 3.93e-01 | 0.0595 |
| 8175 | SF3A2 | LZE22T | Human | Esophagus | ESCC | 4.71e-07 | 6.32e-01 | 0.068 |
| 8175 | SF3A2 | LZE24T | Human | Esophagus | ESCC | 1.44e-30 | 7.89e-01 | 0.0596 |
| 8175 | SF3A2 | LZE21T | Human | Esophagus | ESCC | 3.39e-08 | 7.44e-01 | 0.0655 |
| 8175 | SF3A2 | LZE6T | Human | Esophagus | ESCC | 5.78e-10 | 3.91e-01 | 0.0845 |
| 8175 | SF3A2 | P1T-E | Human | Esophagus | ESCC | 2.54e-22 | 8.41e-01 | 0.0875 |
| 8175 | SF3A2 | P2T-E | Human | Esophagus | ESCC | 4.63e-48 | 9.18e-01 | 0.1177 |
| 8175 | SF3A2 | P4T-E | Human | Esophagus | ESCC | 2.70e-41 | 8.90e-01 | 0.1323 |
| 8175 | SF3A2 | P5T-E | Human | Esophagus | ESCC | 8.46e-54 | 9.36e-01 | 0.1327 |
| 8175 | SF3A2 | P8T-E | Human | Esophagus | ESCC | 1.32e-24 | 5.69e-01 | 0.0889 |
| Page: 1 2 3 4 5 6 7 |
| 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: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:0022618 | Colorectum | AD | ribonucleoprotein complex assembly | 92/3918 | 220/18723 | 1.49e-12 | 2.60e-10 | 92 |
| GO:0071826 | Colorectum | AD | ribonucleoprotein complex subunit organization | 94/3918 | 227/18723 | 1.70e-12 | 2.87e-10 | 94 |
| GO:0022613 | Colorectum | AD | ribonucleoprotein complex biogenesis | 151/3918 | 463/18723 | 1.96e-09 | 1.39e-07 | 151 |
| GO:0000245 | Colorectum | AD | spliceosomal complex assembly | 33/3918 | 79/18723 | 2.15e-05 | 4.33e-04 | 33 |
| GO:0010975 | Colorectum | AD | regulation of neuron projection development | 129/3918 | 445/18723 | 2.88e-05 | 5.37e-04 | 129 |
| GO:0031346 | Colorectum | AD | positive regulation of cell projection organization | 104/3918 | 353/18723 | 8.26e-05 | 1.30e-03 | 104 |
| GO:0006376 | Colorectum | AD | mRNA splice site selection | 18/3918 | 49/18723 | 7.93e-03 | 4.73e-02 | 18 |
| GO:00083802 | Colorectum | MSS | RNA splicing | 159/3467 | 434/18723 | 1.75e-19 | 1.22e-16 | 159 |
| 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:00718262 | Colorectum | MSS | ribonucleoprotein complex subunit organization | 90/3467 | 227/18723 | 6.88e-14 | 1.78e-11 | 90 |
| GO:00226182 | Colorectum | MSS | ribonucleoprotein complex assembly | 88/3467 | 220/18723 | 7.12e-14 | 1.78e-11 | 88 |
| GO:00226132 | Colorectum | MSS | ribonucleoprotein complex biogenesis | 144/3467 | 463/18723 | 2.76e-11 | 3.67e-09 | 144 |
| GO:00002451 | Colorectum | MSS | spliceosomal complex assembly | 31/3467 | 79/18723 | 1.33e-05 | 3.07e-04 | 31 |
| GO:00313462 | Colorectum | MSS | positive regulation of cell projection organization | 96/3467 | 353/18723 | 3.44e-05 | 6.70e-04 | 96 |
| Page: 1 2 3 4 5 6 |
| 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 |
| SF3A2 | SNV | Missense_Mutation | novel | c.1004N>C | p.Gly335Ala | p.G335A | Q15428 | protein_coding | deleterious_low_confidence(0.01) | benign(0) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
| SF3A2 | SNV | Missense_Mutation | c.527N>G | p.Tyr176Cys | p.Y176C | Q15428 | protein_coding | deleterious_low_confidence(0.02) | possibly_damaging(0.715) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD | |
| SF3A2 | insertion | Frame_Shift_Ins | novel | c.687_688insCCAAT | p.Val230ProfsTer3 | p.V230Pfs*3 | Q15428 | protein_coding | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| SF3A2 | insertion | Frame_Shift_Ins | novel | c.688_689insAGAAGGGAGGCCGGCAGGGC | p.Val230GlufsTer8 | p.V230Efs*8 | Q15428 | protein_coding | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | ||
| SF3A2 | SNV | Missense_Mutation | novel | c.1069G>T | p.Val357Phe | p.V357F | Q15428 | protein_coding | tolerated_low_confidence(0.27) | benign(0.193) | TCGA-VS-A8EJ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
| SF3A2 | SNV | Missense_Mutation | novel | c.443N>A | p.Arg148His | p.R148H | Q15428 | protein_coding | deleterious_low_confidence(0.03) | probably_damaging(0.951) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SF3A2 | SNV | Missense_Mutation | c.610N>G | p.Lys204Glu | p.K204E | Q15428 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.939) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| SF3A2 | SNV | Missense_Mutation | c.461N>T | p.Ala154Val | p.A154V | Q15428 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.97) | TCGA-AA-A01R-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD | |
| SF3A2 | SNV | Missense_Mutation | c.382N>A | p.Gly128Ser | p.G128S | Q15428 | protein_coding | tolerated_low_confidence(0.05) | possibly_damaging(0.527) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SF3A2 | SNV | Missense_Mutation | c.431N>A | p.Gly144Asp | p.G144D | Q15428 | protein_coding | tolerated_low_confidence(0.24) | benign(0.149) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
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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 |
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