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Gene: PDXDC1 |
Gene summary for PDXDC1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PDXDC1 | Gene ID | 23042 |
Gene name | pyridoxal dependent decarboxylase domain containing 1 | |
Gene Alias | LP8165 | |
Cytomap | 16p13.11 | |
Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | Q6P996 |
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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 |
23042 | PDXDC1 | P54T-E | Human | Esophagus | ESCC | 6.56e-26 | 4.17e-01 | 0.0975 |
23042 | PDXDC1 | P57T-E | Human | Esophagus | ESCC | 1.99e-15 | 3.01e-01 | 0.0926 |
23042 | PDXDC1 | P61T-E | Human | Esophagus | ESCC | 7.60e-15 | 3.97e-01 | 0.099 |
23042 | PDXDC1 | P62T-E | Human | Esophagus | ESCC | 1.99e-32 | 6.99e-01 | 0.1302 |
23042 | PDXDC1 | P65T-E | Human | Esophagus | ESCC | 1.25e-15 | 1.90e-01 | 0.0978 |
23042 | PDXDC1 | P74T-E | Human | Esophagus | ESCC | 8.55e-20 | 5.56e-01 | 0.1479 |
23042 | PDXDC1 | P75T-E | Human | Esophagus | ESCC | 2.27e-30 | 6.42e-01 | 0.1125 |
23042 | PDXDC1 | P76T-E | Human | Esophagus | ESCC | 3.03e-20 | 2.30e-01 | 0.1207 |
23042 | PDXDC1 | P79T-E | Human | Esophagus | ESCC | 1.52e-17 | 2.23e-01 | 0.1154 |
23042 | PDXDC1 | P80T-E | Human | Esophagus | ESCC | 6.38e-16 | 5.92e-01 | 0.155 |
23042 | PDXDC1 | P82T-E | Human | Esophagus | ESCC | 1.47e-13 | 9.39e-01 | 0.1072 |
23042 | PDXDC1 | P83T-E | Human | Esophagus | ESCC | 2.03e-18 | 6.16e-01 | 0.1738 |
23042 | PDXDC1 | P84T-E | Human | Esophagus | ESCC | 2.00e-11 | 3.09e-01 | 0.0933 |
23042 | PDXDC1 | P89T-E | Human | Esophagus | ESCC | 5.69e-03 | 5.32e-01 | 0.1752 |
23042 | PDXDC1 | P91T-E | Human | Esophagus | ESCC | 5.21e-06 | 4.58e-01 | 0.1828 |
23042 | PDXDC1 | P104T-E | Human | Esophagus | ESCC | 1.84e-09 | 8.70e-01 | 0.0931 |
23042 | PDXDC1 | P107T-E | Human | Esophagus | ESCC | 3.77e-23 | 5.87e-01 | 0.171 |
23042 | PDXDC1 | P127T-E | Human | Esophagus | ESCC | 2.08e-17 | 3.24e-01 | 0.0826 |
23042 | PDXDC1 | P128T-E | Human | Esophagus | ESCC | 1.90e-22 | 7.49e-01 | 0.1241 |
23042 | PDXDC1 | P130T-E | Human | Esophagus | ESCC | 1.65e-24 | 6.16e-01 | 0.1676 |
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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 |
PDXDC1 | SNV | Missense_Mutation | c.881N>A | p.Ser294Asn | p.S294N | Q6P996 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PDXDC1 | SNV | Missense_Mutation | c.1006C>T | p.Leu336Phe | p.L336F | Q6P996 | protein_coding | deleterious(0) | probably_damaging(0.992) | TCGA-AR-A1AI-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | PD | |
PDXDC1 | SNV | Missense_Mutation | c.496N>C | p.Phe166Leu | p.F166L | Q6P996 | protein_coding | deleterious(0.01) | possibly_damaging(0.559) | TCGA-BH-A0DL-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR | |
PDXDC1 | SNV | Missense_Mutation | novel | c.93N>C | p.Gln31His | p.Q31H | Q6P996 | protein_coding | deleterious(0.03) | benign(0.014) | TCGA-EW-A6SD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tch | SD |
PDXDC1 | SNV | Missense_Mutation | novel | c.1768N>A | p.Glu590Lys | p.E590K | Q6P996 | protein_coding | tolerated(0.21) | possibly_damaging(0.576) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
PDXDC1 | insertion | Frame_Shift_Ins | novel | c.2145_2146insATCTTGGTAGCCGTGGGATTCA | p.Ala716IlefsTer11 | p.A716Ifs*11 | Q6P996 | protein_coding | TCGA-A8-A08Z-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | ||
PDXDC1 | insertion | Frame_Shift_Ins | novel | c.1656_1657insGTATCTTACCATTTCGGTCGAAC | p.Asn553ValfsTer15 | p.N553Vfs*15 | Q6P996 | protein_coding | TCGA-A8-A09D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR | ||
PDXDC1 | insertion | Frame_Shift_Ins | novel | c.862_863insAA | p.Ala288GlufsTer9 | p.A288Efs*9 | Q6P996 | protein_coding | TCGA-AN-A03X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
PDXDC1 | insertion | Nonsense_Mutation | novel | c.373_374insAATATAATATATAA | p.Leu125GlnfsTer5 | p.L125Qfs*5 | Q6P996 | protein_coding | TCGA-AO-A03R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
PDXDC1 | SNV | Missense_Mutation | novel | c.519G>T | p.Lys173Asn | p.K173N | Q6P996 | protein_coding | tolerated(0.16) | benign(0.003) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | 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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