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Gene: SH2D3A |
Gene summary for SH2D3A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SH2D3A | Gene ID | 10045 |
| Gene name | SH2 domain containing 3A | |
| Gene Alias | NSP1 | |
| Cytomap | 19p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | A8K2M8 |
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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 |
| 10045 | SH2D3A | LZE5T | Human | Esophagus | ESCC | 1.12e-04 | 2.06e-01 | 0.0514 |
| 10045 | SH2D3A | LZE24T | Human | Esophagus | ESCC | 1.98e-23 | 6.20e-01 | 0.0596 |
| 10045 | SH2D3A | LZE21T | Human | Esophagus | ESCC | 5.46e-03 | 2.70e-01 | 0.0655 |
| 10045 | SH2D3A | P1T-E | Human | Esophagus | ESCC | 5.18e-12 | 5.40e-01 | 0.0875 |
| 10045 | SH2D3A | P2T-E | Human | Esophagus | ESCC | 1.12e-09 | 1.19e-01 | 0.1177 |
| 10045 | SH2D3A | P4T-E | Human | Esophagus | ESCC | 2.71e-05 | 1.55e-01 | 0.1323 |
| 10045 | SH2D3A | P5T-E | Human | Esophagus | ESCC | 2.22e-09 | 1.91e-01 | 0.1327 |
| 10045 | SH2D3A | P8T-E | Human | Esophagus | ESCC | 6.06e-25 | 6.39e-01 | 0.0889 |
| 10045 | SH2D3A | P9T-E | Human | Esophagus | ESCC | 3.03e-09 | 2.23e-01 | 0.1131 |
| 10045 | SH2D3A | P10T-E | Human | Esophagus | ESCC | 1.24e-14 | 3.76e-01 | 0.116 |
| 10045 | SH2D3A | P11T-E | Human | Esophagus | ESCC | 7.87e-08 | 2.75e-01 | 0.1426 |
| 10045 | SH2D3A | P12T-E | Human | Esophagus | ESCC | 2.00e-11 | 2.27e-01 | 0.1122 |
| 10045 | SH2D3A | P15T-E | Human | Esophagus | ESCC | 4.69e-15 | 3.32e-01 | 0.1149 |
| 10045 | SH2D3A | P16T-E | Human | Esophagus | ESCC | 1.69e-05 | 7.21e-02 | 0.1153 |
| 10045 | SH2D3A | P17T-E | Human | Esophagus | ESCC | 1.63e-15 | 4.48e-01 | 0.1278 |
| 10045 | SH2D3A | P20T-E | Human | Esophagus | ESCC | 1.33e-11 | 1.10e-01 | 0.1124 |
| 10045 | SH2D3A | P21T-E | Human | Esophagus | ESCC | 1.64e-18 | 2.63e-01 | 0.1617 |
| 10045 | SH2D3A | P22T-E | Human | Esophagus | ESCC | 8.45e-08 | 7.09e-02 | 0.1236 |
| 10045 | SH2D3A | P23T-E | Human | Esophagus | ESCC | 7.03e-23 | 6.25e-01 | 0.108 |
| 10045 | SH2D3A | P24T-E | Human | Esophagus | ESCC | 9.30e-09 | 2.90e-01 | 0.1287 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| 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 |
| ∗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:003109818 | Esophagus | ESCC | stress-activated protein kinase signaling cascade | 154/8552 | 247/18723 | 8.53e-08 | 1.44e-06 | 154 |
| GO:005140318 | Esophagus | ESCC | stress-activated MAPK cascade | 147/8552 | 239/18723 | 5.43e-07 | 7.18e-06 | 147 |
| GO:00182099 | Esophagus | ESCC | peptidyl-serine modification | 196/8552 | 338/18723 | 3.07e-06 | 3.47e-05 | 196 |
| GO:001810515 | Esophagus | ESCC | peptidyl-serine phosphorylation | 184/8552 | 315/18723 | 3.22e-06 | 3.61e-05 | 184 |
| GO:00072549 | Esophagus | ESCC | JNK cascade | 102/8552 | 167/18723 | 4.22e-05 | 3.39e-04 | 102 |
| GO:00331355 | Esophagus | ESCC | regulation of peptidyl-serine phosphorylation | 81/8552 | 144/18723 | 6.79e-03 | 2.48e-02 | 81 |
| GO:00331383 | Esophagus | ESCC | positive regulation of peptidyl-serine phosphorylation | 61/8552 | 108/18723 | 1.54e-02 | 4.96e-02 | 61 |
| GO:003109816 | Oral cavity | OSCC | stress-activated protein kinase signaling cascade | 141/7305 | 247/18723 | 5.74e-09 | 1.25e-07 | 141 |
| GO:005140316 | Oral cavity | OSCC | stress-activated MAPK cascade | 134/7305 | 239/18723 | 6.02e-08 | 1.09e-06 | 134 |
| GO:00182098 | Oral cavity | OSCC | peptidyl-serine modification | 175/7305 | 338/18723 | 1.09e-06 | 1.46e-05 | 175 |
| GO:001810510 | Oral cavity | OSCC | peptidyl-serine phosphorylation | 164/7305 | 315/18723 | 1.51e-06 | 1.99e-05 | 164 |
| GO:00072548 | Oral cavity | OSCC | JNK cascade | 90/7305 | 167/18723 | 6.49e-05 | 5.26e-04 | 90 |
| GO:00331354 | Oral cavity | OSCC | regulation of peptidyl-serine phosphorylation | 72/7305 | 144/18723 | 4.66e-03 | 1.87e-02 | 72 |
| GO:0033138 | Oral cavity | OSCC | positive regulation of peptidyl-serine phosphorylation | 55/7305 | 108/18723 | 7.75e-03 | 2.84e-02 | 55 |
| GO:003109825 | Skin | cSCC | stress-activated protein kinase signaling cascade | 92/4864 | 247/18723 | 5.78e-05 | 5.74e-04 | 92 |
| GO:005140325 | Skin | cSCC | stress-activated MAPK cascade | 88/4864 | 239/18723 | 1.32e-04 | 1.20e-03 | 88 |
| GO:000725423 | Skin | cSCC | JNK cascade | 60/4864 | 167/18723 | 2.77e-03 | 1.56e-02 | 60 |
| GO:001820923 | Skin | cSCC | peptidyl-serine modification | 108/4864 | 338/18723 | 7.73e-03 | 3.60e-02 | 108 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
| SH2D3A | SNV | Missense_Mutation | c.1369N>G | p.Leu457Val | p.L457V | Q9BRG2 | protein_coding | deleterious(0.01) | probably_damaging(0.998) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SH2D3A | SNV | Missense_Mutation | novel | c.1077G>C | p.Leu359Phe | p.L359F | Q9BRG2 | protein_coding | deleterious(0.04) | benign(0.437) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| SH2D3A | SNV | Missense_Mutation | rs757778461 | c.1292C>T | p.Thr431Met | p.T431M | Q9BRG2 | protein_coding | deleterious(0.04) | probably_damaging(0.999) | TCGA-AR-A1AO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| SH2D3A | insertion | Frame_Shift_Ins | novel | c.1580_1581insGGGAGATGGAGTCTGCAGTGAGCTGAGA | p.Asn528GlyfsTer10 | p.N528Gfs*10 | Q9BRG2 | protein_coding | TCGA-A2-A0CP-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| SH2D3A | SNV | Missense_Mutation | rs754176794 | c.52N>A | p.Gly18Ser | p.G18S | Q9BRG2 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SH2D3A | SNV | Missense_Mutation | rs754330790 | c.674N>G | p.Ser225Cys | p.S225C | Q9BRG2 | protein_coding | deleterious(0.03) | benign(0.417) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| SH2D3A | SNV | Missense_Mutation | rs372429785 | c.365G>A | p.Arg122His | p.R122H | Q9BRG2 | protein_coding | tolerated(0.09) | benign(0.007) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| SH2D3A | SNV | Missense_Mutation | novel | c.980N>T | p.Gln327Leu | p.Q327L | Q9BRG2 | protein_coding | deleterious(0.04) | possibly_damaging(0.617) | TCGA-VS-A959-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| SH2D3A | SNV | Missense_Mutation | rs765407222 | c.376N>A | p.Glu126Lys | p.E126K | Q9BRG2 | protein_coding | tolerated(0.08) | benign(0.119) | TCGA-AA-3950-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SH2D3A | SNV | Missense_Mutation | c.1051C>T | p.Leu351Phe | p.L351F | Q9BRG2 | protein_coding | deleterious(0.03) | probably_damaging(0.946) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR |
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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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