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Gene: PDZRN4 |
Gene summary for PDZRN4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PDZRN4 | Gene ID | 29951 |
Gene name | PDZ domain containing ring finger 4 | |
Gene Alias | LNX4 | |
Cytomap | 12q12 | |
Gene Type | protein-coding | GO ID | GO:0003674 | UniProtAcc | B4DGD1 |
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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 |
29951 | PDZRN4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.88e-04 | 1.77e-01 | 0.0155 |
29951 | PDZRN4 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.59e-03 | 1.74e-01 | -0.1954 |
29951 | PDZRN4 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.27e-03 | 1.61e-01 | -0.1207 |
29951 | PDZRN4 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.66e-04 | 1.46e-01 | -0.1464 |
29951 | PDZRN4 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.94e-04 | 2.35e-01 | -0.059 |
29951 | PDZRN4 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.25e-03 | 3.90e-01 | -0.1706 |
29951 | PDZRN4 | HTA11_546_2000001011 | Human | Colorectum | AD | 7.42e-04 | 2.15e-01 | -0.0842 |
29951 | PDZRN4 | HTA11_99999965104_69814 | Human | Colorectum | MSS | 1.33e-82 | 3.95e+00 | 0.281 |
29951 | PDZRN4 | HTA11_99999974143_84620 | Human | Colorectum | MSS | 4.21e-19 | 5.26e-01 | 0.3005 |
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Transcriptomic changes along malignancy continuum. |
∗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). |
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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 |
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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 |
PDZRN4 | SNV | Missense_Mutation | novel | c.1373G>T | p.Gly458Val | p.G458V | Q6ZMN7 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-60-2724-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Chemotherapy | cisplatin | SD |
PDZRN4 | SNV | Missense_Mutation | c.970N>T | p.Ala324Ser | p.A324S | Q6ZMN7 | protein_coding | tolerated(0.68) | benign(0.001) | TCGA-63-5128-01 | Lung | lung squamous cell carcinoma | Male | Unknown | I/II | Unknown | Unknown | PD | |
PDZRN4 | SNV | Missense_Mutation | c.794N>A | p.Gly265Glu | p.G265E | Q6ZMN7 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-63-5131-01 | Lung | lung squamous cell carcinoma | Male | Unknown | I/II | Unknown | Unknown | SD | |
PDZRN4 | SNV | Missense_Mutation | c.2300C>A | p.Thr767Asn | p.T767N | Q6ZMN7 | protein_coding | tolerated(0.08) | probably_damaging(0.937) | TCGA-66-2757-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Chemotherapy | gemcitabine | PD | |
PDZRN4 | SNV | Missense_Mutation | c.2494N>T | p.Pro832Ser | p.P832S | Q6ZMN7 | protein_coding | tolerated(0.28) | benign(0.133) | TCGA-70-6722-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Unknown | Unknown | PD | |
PDZRN4 | SNV | Missense_Mutation | novel | c.1823N>A | p.Ser608Tyr | p.S608Y | Q6ZMN7 | protein_coding | deleterious(0) | possibly_damaging(0.556) | TCGA-77-7142-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PDZRN4 | SNV | Missense_Mutation | novel | c.2121N>A | p.Phe707Leu | p.F707L | Q6ZMN7 | protein_coding | tolerated(0.52) | benign(0.01) | TCGA-77-7142-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PDZRN4 | SNV | Missense_Mutation | novel | c.1930G>A | p.Asp644Asn | p.D644N | Q6ZMN7 | protein_coding | tolerated(0.2) | probably_damaging(0.91) | TCGA-77-8009-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
PDZRN4 | SNV | Missense_Mutation | c.1987N>C | p.Glu663Gln | p.E663Q | Q6ZMN7 | protein_coding | tolerated(0.39) | benign(0.28) | TCGA-85-6560-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | cisplatin | SD | |
PDZRN4 | SNV | Missense_Mutation | novel | c.2869N>T | p.Arg957Cys | p.R957C | Q6ZMN7 | protein_coding | deleterious(0.02) | probably_damaging(0.994) | TCGA-94-A4VJ-01 | Lung | lung squamous cell carcinoma | Female | >=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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