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Gene: SF3A3 |
Gene summary for SF3A3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SF3A3 | Gene ID | 10946 |
Gene name | splicing factor 3a subunit 3 | |
Gene Alias | PRP9 | |
Cytomap | 1p34.3 | |
Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | B4DW90 |
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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 |
10946 | SF3A3 | P47T-E | Human | Esophagus | ESCC | 3.04e-09 | 1.75e-01 | 0.1067 |
10946 | SF3A3 | P48T-E | Human | Esophagus | ESCC | 2.87e-17 | 3.70e-01 | 0.0959 |
10946 | SF3A3 | P49T-E | Human | Esophagus | ESCC | 2.86e-12 | 1.29e+00 | 0.1768 |
10946 | SF3A3 | P52T-E | Human | Esophagus | ESCC | 9.04e-36 | 9.14e-01 | 0.1555 |
10946 | SF3A3 | P54T-E | Human | Esophagus | ESCC | 1.65e-19 | 6.06e-01 | 0.0975 |
10946 | SF3A3 | P56T-E | Human | Esophagus | ESCC | 8.15e-12 | 1.32e+00 | 0.1613 |
10946 | SF3A3 | P57T-E | Human | Esophagus | ESCC | 5.25e-17 | 4.07e-01 | 0.0926 |
10946 | SF3A3 | P61T-E | Human | Esophagus | ESCC | 1.04e-19 | 4.10e-01 | 0.099 |
10946 | SF3A3 | P62T-E | Human | Esophagus | ESCC | 1.71e-53 | 9.43e-01 | 0.1302 |
10946 | SF3A3 | P65T-E | Human | Esophagus | ESCC | 1.77e-28 | 5.06e-01 | 0.0978 |
10946 | SF3A3 | P74T-E | Human | Esophagus | ESCC | 1.34e-34 | 1.09e+00 | 0.1479 |
10946 | SF3A3 | P75T-E | Human | Esophagus | ESCC | 3.16e-46 | 1.03e+00 | 0.1125 |
10946 | SF3A3 | P76T-E | Human | Esophagus | ESCC | 6.57e-40 | 8.96e-01 | 0.1207 |
10946 | SF3A3 | P79T-E | Human | Esophagus | ESCC | 5.34e-34 | 7.50e-01 | 0.1154 |
10946 | SF3A3 | P80T-E | Human | Esophagus | ESCC | 2.39e-29 | 9.66e-01 | 0.155 |
10946 | SF3A3 | P82T-E | Human | Esophagus | ESCC | 2.23e-19 | 1.08e+00 | 0.1072 |
10946 | SF3A3 | P83T-E | Human | Esophagus | ESCC | 9.65e-37 | 1.24e+00 | 0.1738 |
10946 | SF3A3 | P84T-E | Human | Esophagus | ESCC | 6.68e-10 | 4.67e-01 | 0.0933 |
10946 | SF3A3 | P89T-E | Human | Esophagus | ESCC | 1.62e-13 | 1.02e+00 | 0.1752 |
10946 | SF3A3 | P91T-E | Human | Esophagus | ESCC | 7.00e-12 | 1.76e+00 | 0.1828 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000838026 | Esophagus | HGIN | RNA splicing | 160/2587 | 434/18723 | 3.74e-34 | 1.12e-30 | 160 |
GO:002261327 | Esophagus | HGIN | ribonucleoprotein complex biogenesis | 158/2587 | 463/18723 | 2.61e-29 | 5.23e-26 | 158 |
GO:000037520 | Esophagus | HGIN | RNA splicing, via transesterification reactions | 115/2587 | 324/18723 | 3.16e-23 | 3.80e-20 | 115 |
GO:000037720 | Esophagus | HGIN | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 113/2587 | 320/18723 | 1.24e-22 | 9.26e-20 | 113 |
GO:000039820 | Esophagus | HGIN | mRNA splicing, via spliceosome | 113/2587 | 320/18723 | 1.24e-22 | 9.26e-20 | 113 |
GO:007182627 | Esophagus | HGIN | ribonucleoprotein complex subunit organization | 84/2587 | 227/18723 | 1.34e-18 | 5.37e-16 | 84 |
GO:002261827 | Esophagus | HGIN | ribonucleoprotein complex assembly | 82/2587 | 220/18723 | 2.07e-18 | 7.36e-16 | 82 |
GO:00002457 | Esophagus | HGIN | spliceosomal complex assembly | 25/2587 | 79/18723 | 3.74e-05 | 9.30e-04 | 25 |
GO:00063764 | Esophagus | HGIN | mRNA splice site selection | 15/2587 | 49/18723 | 1.88e-03 | 2.01e-02 | 15 |
GO:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
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:0071826111 | Esophagus | ESCC | ribonucleoprotein complex subunit organization | 166/8552 | 227/18723 | 2.94e-17 | 2.42e-15 | 166 |
GO:0022618111 | Esophagus | ESCC | ribonucleoprotein complex assembly | 159/8552 | 220/18723 | 8.19e-16 | 5.71e-14 | 159 |
GO:000024514 | Esophagus | ESCC | spliceosomal complex assembly | 48/8552 | 79/18723 | 4.93e-03 | 1.89e-02 | 48 |
GO:000838012 | Liver | Cirrhotic | RNA splicing | 229/4634 | 434/18723 | 9.13e-37 | 2.86e-33 | 229 |
GO:002261312 | Liver | Cirrhotic | ribonucleoprotein complex biogenesis | 231/4634 | 463/18723 | 3.28e-32 | 6.86e-29 | 231 |
GO:000037512 | Liver | Cirrhotic | RNA splicing, via transesterification reactions | 175/4634 | 324/18723 | 5.95e-30 | 7.47e-27 | 175 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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 |
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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 |
SF3A3 | SNV | Missense_Mutation | novel | c.260N>C | p.Arg87Thr | p.R87T | Q12874 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-3C-AALI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Poly E | Complete Response |
SF3A3 | SNV | Missense_Mutation | c.644N>T | p.Ala215Val | p.A215V | Q12874 | protein_coding | tolerated(0.18) | benign(0) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
SF3A3 | insertion | Frame_Shift_Ins | novel | c.751_752insTAATGGAACTTATGGTCATATGGGAAAAACAGACAAATAAG | p.Ser251LeufsTer27 | p.S251Lfs*27 | Q12874 | protein_coding | TCGA-C8-A1HE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
SF3A3 | deletion | Frame_Shift_Del | novel | c.693delA | p.Glu232ArgfsTer6 | p.E232Rfs*6 | Q12874 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
SF3A3 | deletion | Frame_Shift_Del | novel | c.1308delG | p.Arg436SerfsTer14 | p.R436Sfs*14 | Q12874 | protein_coding | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD | ||
SF3A3 | SNV | Missense_Mutation | novel | c.184N>A | p.Asp62Asn | p.D62N | Q12874 | protein_coding | tolerated(0.1) | benign(0.035) | TCGA-C5-A2LY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
SF3A3 | SNV | Missense_Mutation | novel | c.6G>C | p.Glu2Asp | p.E2D | Q12874 | protein_coding | tolerated(0.3) | probably_damaging(0.956) | TCGA-C5-A3HF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
SF3A3 | SNV | Missense_Mutation | c.816N>C | p.Leu272Phe | p.L272F | Q12874 | protein_coding | deleterious(0) | possibly_damaging(0.783) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
SF3A3 | SNV | Missense_Mutation | novel | c.646N>A | p.Glu216Lys | p.E216K | Q12874 | protein_coding | tolerated(0.08) | benign(0.01) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
SF3A3 | SNV | Missense_Mutation | novel | c.142N>A | p.Asp48Asn | p.D48N | Q12874 | protein_coding | deleterious(0.03) | benign(0.226) | TCGA-ZJ-AAXT-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
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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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