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Gene: PSD4 |
Gene summary for PSD4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PSD4 | Gene ID | 23550 |
| Gene name | pleckstrin and Sec7 domain containing 4 | |
| Gene Alias | EFA6B | |
| Cytomap | 2q14.1 | |
| Gene Type | protein-coding | GO ID | GO:0007154 | UniProtAcc | Q8NDX1 |
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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 |
| 23550 | PSD4 | C04 | Human | Oral cavity | OSCC | 4.13e-13 | 7.12e-01 | 0.2633 |
| 23550 | PSD4 | C21 | Human | Oral cavity | OSCC | 2.83e-17 | 5.87e-01 | 0.2678 |
| 23550 | PSD4 | C30 | Human | Oral cavity | OSCC | 2.28e-19 | 6.84e-01 | 0.3055 |
| 23550 | PSD4 | C38 | Human | Oral cavity | OSCC | 3.16e-04 | 6.37e-01 | 0.172 |
| 23550 | PSD4 | C43 | Human | Oral cavity | OSCC | 5.21e-08 | 2.39e-01 | 0.1704 |
| 23550 | PSD4 | C46 | Human | Oral cavity | OSCC | 1.27e-10 | 2.47e-01 | 0.1673 |
| 23550 | PSD4 | C51 | Human | Oral cavity | OSCC | 1.92e-05 | 4.01e-01 | 0.2674 |
| 23550 | PSD4 | C57 | Human | Oral cavity | OSCC | 1.29e-16 | 3.61e-01 | 0.1679 |
| 23550 | PSD4 | C06 | Human | Oral cavity | OSCC | 1.55e-09 | 5.99e-01 | 0.2699 |
| 23550 | PSD4 | C08 | Human | Oral cavity | OSCC | 3.66e-04 | 1.06e-01 | 0.1919 |
| 23550 | PSD4 | C09 | Human | Oral cavity | OSCC | 9.90e-03 | 6.56e-02 | 0.1431 |
| 23550 | PSD4 | LN22 | Human | Oral cavity | OSCC | 4.97e-06 | 4.74e-01 | 0.1733 |
| 23550 | PSD4 | LN46 | Human | Oral cavity | OSCC | 5.99e-06 | 3.53e-01 | 0.1666 |
| 23550 | PSD4 | LP17 | Human | Oral cavity | LP | 2.23e-04 | 5.56e-01 | 0.2349 |
| 23550 | PSD4 | SYSMH1 | Human | Oral cavity | OSCC | 1.44e-06 | 2.07e-01 | 0.1127 |
| 23550 | PSD4 | SYSMH2 | Human | Oral cavity | OSCC | 6.56e-06 | 1.96e-01 | 0.2326 |
| 23550 | PSD4 | SYSMH3 | Human | Oral cavity | OSCC | 1.09e-07 | 2.54e-01 | 0.2442 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma |
| ∗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:00072659 | Oral cavity | OSCC | Ras protein signal transduction | 185/7305 | 337/18723 | 1.95e-09 | 4.60e-08 | 185 |
| GO:00465788 | Oral cavity | OSCC | regulation of Ras protein signal transduction | 90/7305 | 189/18723 | 9.58e-03 | 3.40e-02 | 90 |
| GO:000726515 | Oral cavity | LP | Ras protein signal transduction | 109/4623 | 337/18723 | 8.44e-04 | 7.36e-03 | 109 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0414427 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
| hsa04144112 | Oral cavity | OSCC | Endocytosis | 174/3704 | 251/8465 | 9.42e-17 | 4.51e-15 | 2.29e-15 | 174 |
| hsa0414428 | Oral cavity | LP | Endocytosis | 121/2418 | 251/8465 | 1.89e-11 | 3.70e-10 | 2.38e-10 | 121 |
| hsa0414436 | Oral cavity | LP | Endocytosis | 121/2418 | 251/8465 | 1.89e-11 | 3.70e-10 | 2.38e-10 | 121 |
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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. |
| 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 |
| PSD4 | SNV | Missense_Mutation | c.2387N>T | p.Thr796Met | p.T796M | Q8NDX1 | protein_coding | deleterious(0.01) | probably_damaging(0.987) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PSD4 | SNV | Missense_Mutation | novel | c.1924N>G | p.Phe642Val | p.F642V | Q8NDX1 | protein_coding | deleterious(0.01) | possibly_damaging(0.644) | TCGA-AQ-A7U7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Targeted Molecular therapy | rituximab | CR |
| PSD4 | SNV | Missense_Mutation | c.788N>C | p.Gly263Ala | p.G263A | Q8NDX1 | protein_coding | tolerated_low_confidence(0.28) | benign(0.003) | TCGA-D8-A1JM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | ChemotherapyHormone Therapy | doxorubicine | SD | |
| PSD4 | SNV | Missense_Mutation | rs368039539 | c.569C>T | p.Thr190Met | p.T190M | Q8NDX1 | protein_coding | tolerated_low_confidence(0.06) | benign(0.015) | TCGA-D8-A3Z6-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphane | SD |
| PSD4 | insertion | Frame_Shift_Ins | novel | c.1113_1114insCCCCACCCAGCTAATTTTTGTATTTTTAGTAGAGATAGGTT | p.Trp372ProfsTer52 | p.W372Pfs*52 | Q8NDX1 | protein_coding | TCGA-AN-A0FD-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
| PSD4 | insertion | Frame_Shift_Ins | novel | c.794_795insGAGCACGTCCACACAGGTAGTGTTCTGGGCAGGCATC | p.Cys265TrpfsTer30 | p.C265Wfs*30 | Q8NDX1 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| PSD4 | insertion | Frame_Shift_Ins | novel | c.2955_2956insGTTTTTGTTTTTGTTTTTGAGACAAAGTCTCGCTCTGTCGCCCAGG | p.Leu986ValfsTer21 | p.L986Vfs*21 | Q8NDX1 | protein_coding | TCGA-BH-A0AY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | SD | |||
| PSD4 | SNV | Missense_Mutation | rs761343089 | c.1391C>T | p.Ser464Leu | p.S464L | Q8NDX1 | protein_coding | deleterious_low_confidence(0) | benign(0.091) | TCGA-Q1-A6DW-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| PSD4 | SNV | Missense_Mutation | novel | c.1311N>C | p.Trp437Cys | p.W437C | Q8NDX1 | protein_coding | tolerated_low_confidence(0.28) | benign(0) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PSD4 | SNV | Missense_Mutation | c.2396G>A | p.Gly799Asp | p.G799D | Q8NDX1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AA-3663-01 | Colorectum | colon 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 |
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