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Gene: PSD4 |
Gene summary for PSD4 |
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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 |
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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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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 |
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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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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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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 |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 | novel | c.2222C>T | p.Ala741Val | p.A741V | Q8NDX1 | protein_coding | tolerated(0.05) | benign(0.033) | TCGA-B5-A1MX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Hormone Therapy | megace | SD |
PSD4 | SNV | Missense_Mutation | novel | c.377N>A | p.Arg126Lys | p.R126K | Q8NDX1 | protein_coding | tolerated_low_confidence(0.32) | benign(0.001) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PSD4 | SNV | Missense_Mutation | novel | c.2400N>T | p.Lys800Asn | p.K800N | Q8NDX1 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PSD4 | SNV | Missense_Mutation | novel | c.2942N>C | p.Leu981Pro | p.L981P | Q8NDX1 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PSD4 | SNV | Missense_Mutation | novel | c.1169N>T | p.Pro390Leu | p.P390L | Q8NDX1 | protein_coding | deleterious_low_confidence(0.02) | benign(0) | TCGA-BG-A222-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PSD4 | SNV | Missense_Mutation | novel | c.1327N>C | p.Ser443Pro | p.S443P | Q8NDX1 | protein_coding | tolerated_low_confidence(0.05) | possibly_damaging(0.641) | TCGA-BK-A6W3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PSD4 | SNV | Missense_Mutation | rs144793297 | c.3151C>T | p.Arg1051Trp | p.R1051W | Q8NDX1 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
PSD4 | SNV | Missense_Mutation | c.1571N>T | p.Ala524Val | p.A524V | Q8NDX1 | protein_coding | tolerated(0.31) | benign(0) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PSD4 | SNV | Missense_Mutation | c.2011N>T | p.Pro671Ser | p.P671S | Q8NDX1 | protein_coding | deleterious(0.01) | possibly_damaging(0.514) | TCGA-D1-A103-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PSD4 | SNV | Missense_Mutation | rs779250912 | c.1207N>T | p.Gly403Cys | p.G403C | Q8NDX1 | protein_coding | deleterious_low_confidence(0.04) | benign(0.005) | TCGA-DF-A2KN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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