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Gene: SH2D4A |
Gene summary for SH2D4A |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SH2D4A | Gene ID | 63898 |
| Gene name | SH2 domain containing 4A | |
| Gene Alias | PPP1R38 | |
| Cytomap | 8p21.3 | |
| Gene Type | protein-coding | GO ID | GO:0005575 | UniProtAcc | Q9H788 |
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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 |
| 63898 | SH2D4A | LZE4T | Human | Esophagus | ESCC | 9.63e-05 | 2.19e-01 | 0.0811 |
| 63898 | SH2D4A | LZE5T | Human | Esophagus | ESCC | 8.35e-04 | 2.48e-01 | 0.0514 |
| 63898 | SH2D4A | LZE8T | Human | Esophagus | ESCC | 3.14e-03 | 1.46e-01 | 0.067 |
| 63898 | SH2D4A | LZE20T | Human | Esophagus | ESCC | 6.18e-05 | 1.76e-01 | 0.0662 |
| 63898 | SH2D4A | LZE24T | Human | Esophagus | ESCC | 7.96e-10 | 3.83e-01 | 0.0596 |
| 63898 | SH2D4A | P1T-E | Human | Esophagus | ESCC | 1.05e-21 | 9.79e-01 | 0.0875 |
| 63898 | SH2D4A | P2T-E | Human | Esophagus | ESCC | 3.27e-09 | 2.48e-01 | 0.1177 |
| 63898 | SH2D4A | P4T-E | Human | Esophagus | ESCC | 6.48e-14 | 4.00e-01 | 0.1323 |
| 63898 | SH2D4A | P5T-E | Human | Esophagus | ESCC | 3.99e-07 | 1.36e-01 | 0.1327 |
| 63898 | SH2D4A | P8T-E | Human | Esophagus | ESCC | 1.64e-19 | 3.91e-01 | 0.0889 |
| 63898 | SH2D4A | P9T-E | Human | Esophagus | ESCC | 7.84e-10 | 2.14e-01 | 0.1131 |
| 63898 | SH2D4A | P10T-E | Human | Esophagus | ESCC | 1.68e-08 | 2.14e-01 | 0.116 |
| 63898 | SH2D4A | P12T-E | Human | Esophagus | ESCC | 3.17e-05 | 6.69e-02 | 0.1122 |
| 63898 | SH2D4A | P17T-E | Human | Esophagus | ESCC | 3.45e-04 | 2.67e-01 | 0.1278 |
| 63898 | SH2D4A | P20T-E | Human | Esophagus | ESCC | 1.74e-13 | 3.20e-01 | 0.1124 |
| 63898 | SH2D4A | P21T-E | Human | Esophagus | ESCC | 6.84e-04 | 1.56e-01 | 0.1617 |
| 63898 | SH2D4A | P22T-E | Human | Esophagus | ESCC | 1.32e-07 | 1.04e-01 | 0.1236 |
| 63898 | SH2D4A | P23T-E | Human | Esophagus | ESCC | 7.98e-19 | 5.61e-01 | 0.108 |
| 63898 | SH2D4A | P24T-E | Human | Esophagus | ESCC | 7.00e-11 | 3.09e-01 | 0.1287 |
| 63898 | SH2D4A | P26T-E | Human | Esophagus | ESCC | 1.99e-14 | 3.26e-01 | 0.1276 |
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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 | ||
| 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 |
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| 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 |
| SH2D4A | SNV | Missense_Mutation | c.245G>T | p.Gly82Val | p.G82V | Q9H788 | protein_coding | deleterious(0) | probably_damaging(0.976) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD | |
| SH2D4A | SNV | Missense_Mutation | c.1022C>T | p.Ser341Leu | p.S341L | Q9H788 | protein_coding | deleterious(0.01) | benign(0.031) | TCGA-A8-A07O-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | CR | ||
| SH2D4A | insertion | Frame_Shift_Ins | novel | c.1170_1171insGCCCGGCTAATTTTTTGTATTTTTAG | p.Cys391AlafsTer111 | p.C391Afs*111 | Q9H788 | protein_coding | TCGA-A7-A0CJ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD | ||
| SH2D4A | SNV | Missense_Mutation | rs761330623 | c.569N>A | p.Arg190His | p.R190H | Q9H788 | protein_coding | tolerated(0.25) | possibly_damaging(0.828) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SH2D4A | SNV | Missense_Mutation | rs368296625 | c.1118N>A | p.Arg373Gln | p.R373Q | Q9H788 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| SH2D4A | SNV | Missense_Mutation | rs754653430 | c.1196C>T | p.Ser399Phe | p.S399F | Q9H788 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-VS-A8QC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | paclitaxel | PD |
| SH2D4A | insertion | Frame_Shift_Ins | novel | c.152_153insTTTTATA | p.Leu52PhefsTer24 | p.L52Ffs*24 | Q9H788 | protein_coding | TCGA-DS-A1OD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | ||
| SH2D4A | SNV | Missense_Mutation | c.809N>A | p.Gly270Asp | p.G270D | Q9H788 | protein_coding | tolerated(0.05) | benign(0.058) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| SH2D4A | SNV | Missense_Mutation | c.455N>G | p.Lys152Arg | p.K152R | Q9H788 | protein_coding | tolerated(0.24) | benign(0.026) | TCGA-AF-4110-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Chemotherapy | oxaliplatin | SD | |
| SH2D4A | SNV | Missense_Mutation | rs769443220 | c.1001N>A | p.Arg334Gln | p.R334Q | Q9H788 | protein_coding | deleterious(0) | probably_damaging(0.95) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | 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 |
| Page: 1 |
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