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Gene: SH3BP4 |
Gene summary for SH3BP4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SH3BP4 | Gene ID | 23677 |
| Gene name | SH3 domain binding protein 4 | |
| Gene Alias | BOG25 | |
| Cytomap | 2q37.2 | |
| Gene Type | protein-coding | GO ID | GO:0001101 | UniProtAcc | Q9P0V3 |
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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 |
| 23677 | SH3BP4 | GSM4909285 | Human | Breast | IDC | 2.62e-02 | -2.16e-01 | 0.21 |
| 23677 | SH3BP4 | GSM4909286 | Human | Breast | IDC | 3.84e-07 | -2.46e-01 | 0.1081 |
| 23677 | SH3BP4 | GSM4909298 | Human | Breast | IDC | 6.82e-05 | 2.00e-01 | 0.1551 |
| 23677 | SH3BP4 | GSM4909309 | Human | Breast | IDC | 5.31e-03 | -2.13e-01 | 0.0483 |
| 23677 | SH3BP4 | GSM4909311 | Human | Breast | IDC | 9.94e-05 | -2.24e-01 | 0.1534 |
| 23677 | SH3BP4 | GSM4909319 | Human | Breast | IDC | 8.08e-07 | -1.92e-01 | 0.1563 |
| 23677 | SH3BP4 | GSM4909321 | Human | Breast | IDC | 3.84e-07 | -2.46e-01 | 0.1559 |
| 23677 | SH3BP4 | brca10 | Human | Breast | Precancer | 3.35e-08 | 5.20e-01 | -0.0029 |
| 23677 | SH3BP4 | NCCBC5 | Human | Breast | DCIS | 2.05e-04 | -2.36e-01 | 0.2046 |
| 23677 | SH3BP4 | DCIS2 | Human | Breast | DCIS | 3.21e-30 | 8.20e-02 | 0.0085 |
| 23677 | SH3BP4 | LZE4T | Human | Esophagus | ESCC | 4.25e-04 | 7.58e-02 | 0.0811 |
| 23677 | SH3BP4 | LZE7T | Human | Esophagus | ESCC | 4.37e-02 | 3.65e-02 | 0.0667 |
| 23677 | SH3BP4 | LZE8T | Human | Esophagus | ESCC | 2.08e-02 | 5.68e-03 | 0.067 |
| 23677 | SH3BP4 | LZE24T | Human | Esophagus | ESCC | 9.10e-10 | 5.33e-01 | 0.0596 |
| 23677 | SH3BP4 | P1T-E | Human | Esophagus | ESCC | 6.47e-08 | 2.04e-01 | 0.0875 |
| 23677 | SH3BP4 | P2T-E | Human | Esophagus | ESCC | 5.87e-23 | 8.10e-02 | 0.1177 |
| 23677 | SH3BP4 | P4T-E | Human | Esophagus | ESCC | 9.26e-07 | 1.92e-01 | 0.1323 |
| 23677 | SH3BP4 | P5T-E | Human | Esophagus | ESCC | 3.97e-17 | 2.35e-01 | 0.1327 |
| 23677 | SH3BP4 | P8T-E | Human | Esophagus | ESCC | 2.12e-19 | 3.10e-01 | 0.0889 |
| 23677 | SH3BP4 | P9T-E | Human | Esophagus | ESCC | 6.67e-08 | 7.69e-02 | 0.1131 |
| Page: 1 2 3 4 5 6 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| ∗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:00513468 | Breast | Precancer | negative regulation of hydrolase activity | 50/1080 | 379/18723 | 3.85e-08 | 2.34e-06 | 50 |
| GO:00098969 | Breast | Precancer | positive regulation of catabolic process | 48/1080 | 492/18723 | 2.62e-04 | 3.84e-03 | 48 |
| GO:00313319 | Breast | Precancer | positive regulation of cellular catabolic process | 43/1080 | 427/18723 | 2.75e-04 | 4.00e-03 | 43 |
| GO:00160497 | Breast | Precancer | cell growth | 46/1080 | 482/18723 | 5.63e-04 | 7.16e-03 | 46 |
| GO:00015587 | Breast | Precancer | regulation of cell growth | 39/1080 | 414/18723 | 1.81e-03 | 1.78e-02 | 39 |
| GO:00011015 | Breast | Precancer | response to acid chemical | 16/1080 | 135/18723 | 4.85e-03 | 3.67e-02 | 16 |
| GO:005134613 | Breast | IDC | negative regulation of hydrolase activity | 71/1434 | 379/18723 | 1.33e-12 | 2.90e-10 | 71 |
| GO:000989614 | Breast | IDC | positive regulation of catabolic process | 62/1434 | 492/18723 | 7.06e-05 | 1.42e-03 | 62 |
| GO:003133114 | Breast | IDC | positive regulation of cellular catabolic process | 54/1434 | 427/18723 | 1.85e-04 | 3.07e-03 | 54 |
| GO:001604913 | Breast | IDC | cell growth | 56/1434 | 482/18723 | 1.16e-03 | 1.26e-02 | 56 |
| GO:000155813 | Breast | IDC | regulation of cell growth | 49/1434 | 414/18723 | 1.55e-03 | 1.55e-02 | 49 |
| GO:000110112 | Breast | IDC | response to acid chemical | 20/1434 | 135/18723 | 3.28e-03 | 2.75e-02 | 20 |
| GO:00432003 | Breast | IDC | response to amino acid | 17/1434 | 116/18723 | 7.13e-03 | 4.92e-02 | 17 |
| GO:005134623 | Breast | DCIS | negative regulation of hydrolase activity | 64/1390 | 379/18723 | 4.32e-10 | 4.80e-08 | 64 |
| GO:000989624 | Breast | DCIS | positive regulation of catabolic process | 61/1390 | 492/18723 | 5.32e-05 | 1.09e-03 | 61 |
| GO:003133124 | Breast | DCIS | positive regulation of cellular catabolic process | 54/1390 | 427/18723 | 8.34e-05 | 1.58e-03 | 54 |
| GO:001604923 | Breast | DCIS | cell growth | 54/1390 | 482/18723 | 1.60e-03 | 1.59e-02 | 54 |
| GO:000155822 | Breast | DCIS | regulation of cell growth | 47/1390 | 414/18723 | 2.39e-03 | 2.16e-02 | 47 |
| GO:000110121 | Breast | DCIS | response to acid chemical | 19/1390 | 135/18723 | 5.17e-03 | 3.81e-02 | 19 |
| GO:0009896111 | Esophagus | ESCC | positive regulation of catabolic process | 332/8552 | 492/18723 | 4.36e-23 | 9.22e-21 | 332 |
| Page: 1 2 3 4 5 6 7 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| 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 |
| SH3BP4 | SNV | Missense_Mutation | novel | c.853N>C | p.Thr285Pro | p.T285P | Q9P0V3 | protein_coding | deleterious(0.04) | possibly_damaging(0.572) | TCGA-A8-A06Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD |
| SH3BP4 | SNV | Missense_Mutation | rs754687295 | c.238N>A | p.Asp80Asn | p.D80N | Q9P0V3 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.969) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
| SH3BP4 | SNV | Missense_Mutation | rs144140235 | c.728N>A | p.Arg243His | p.R243H | Q9P0V3 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AR-A256-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD |
| SH3BP4 | SNV | Missense_Mutation | novel | c.1688N>T | p.Gln563Leu | p.Q563L | Q9P0V3 | protein_coding | deleterious(0.02) | probably_damaging(0.983) | TCGA-B6-A0IN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| SH3BP4 | SNV | Missense_Mutation | c.1442N>G | p.Pro481Arg | p.P481R | Q9P0V3 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-D8-A1XW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD | |
| SH3BP4 | SNV | Missense_Mutation | rs375744207 | c.772G>A | p.Asp258Asn | p.D258N | Q9P0V3 | protein_coding | tolerated(0.64) | benign(0.001) | TCGA-E2-A1LH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| SH3BP4 | SNV | Missense_Mutation | rs773132376 | c.1027N>A | p.Glu343Lys | p.E343K | Q9P0V3 | protein_coding | deleterious(0.03) | benign(0.364) | TCGA-EW-A1IY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD |
| SH3BP4 | SNV | Missense_Mutation | rs376165917 | c.2069N>T | p.Arg690Leu | p.R690L | Q9P0V3 | protein_coding | deleterious(0) | benign(0.131) | TCGA-GM-A3NY-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| SH3BP4 | insertion | Frame_Shift_Ins | novel | c.855_856insCATCAGGTACATGATGTAGTGGTTGGTGGTAAGA | p.Ala286HisfsTer51 | p.A286Hfs*51 | Q9P0V3 | protein_coding | TCGA-A8-A06Y-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD | ||
| SH3BP4 | insertion | In_Frame_Ins | novel | c.1201_1202insGAC | p.Ile401delinsArgLeu | p.I401delinsRL | Q9P0V3 | protein_coding | TCGA-A8-A09W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | 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 |
| Page: 1 |
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