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Gene: AMPD1 |
Gene summary for AMPD1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | AMPD1 | Gene ID | 270 |
Gene name | adenosine monophosphate deaminase 1 | |
Gene Alias | MAD | |
Cytomap | 1p13.2 | |
Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | P23109 |
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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 |
270 | AMPD1 | GSM5353218_PA_PB1B_Pool_1_2_S74_L003 | Human | Prostate | Tumor | 9.05e-11 | 9.42e-01 | 0.1479 |
270 | AMPD1 | GSM5353220_PA_PB1B_Pool_3_S51_L002 | Human | Prostate | Tumor | 1.91e-08 | 9.85e-01 | 0.1531 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
Prostate | BPH: Benign Prostatic Hyperplasia |
∗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 |
GO:000915019 | Prostate | Tumor | purine ribonucleotide metabolic process | 109/3246 | 368/18723 | 3.30e-09 | 1.36e-07 | 109 |
GO:000925918 | Prostate | Tumor | ribonucleotide metabolic process | 110/3246 | 385/18723 | 2.45e-08 | 8.29e-07 | 110 |
GO:000616319 | Prostate | Tumor | purine nucleotide metabolic process | 111/3246 | 396/18723 | 6.46e-08 | 1.88e-06 | 111 |
GO:001969318 | Prostate | Tumor | ribose phosphate metabolic process | 111/3246 | 396/18723 | 6.46e-08 | 1.88e-06 | 111 |
GO:007252119 | Prostate | Tumor | purine-containing compound metabolic process | 115/3246 | 416/18723 | 8.47e-08 | 2.31e-06 | 115 |
GO:000915218 | Prostate | Tumor | purine ribonucleotide biosynthetic process | 53/3246 | 169/18723 | 5.62e-06 | 8.63e-05 | 53 |
GO:000926016 | Prostate | Tumor | ribonucleotide biosynthetic process | 54/3246 | 182/18723 | 2.71e-05 | 3.29e-04 | 54 |
GO:000911718 | Prostate | Tumor | nucleotide metabolic process | 120/3246 | 489/18723 | 2.81e-05 | 3.41e-04 | 120 |
GO:000675317 | Prostate | Tumor | nucleoside phosphate metabolic process | 121/3246 | 497/18723 | 3.81e-05 | 4.41e-04 | 121 |
GO:004639016 | Prostate | Tumor | ribose phosphate biosynthetic process | 55/3246 | 190/18723 | 4.89e-05 | 5.42e-04 | 55 |
GO:007252215 | Prostate | Tumor | purine-containing compound biosynthetic process | 55/3246 | 200/18723 | 2.16e-04 | 1.86e-03 | 55 |
GO:000616415 | Prostate | Tumor | purine nucleotide biosynthetic process | 53/3246 | 191/18723 | 2.18e-04 | 1.87e-03 | 53 |
GO:000916514 | Prostate | Tumor | nucleotide biosynthetic process | 61/3246 | 254/18723 | 4.03e-03 | 2.04e-02 | 61 |
GO:190129314 | Prostate | Tumor | nucleoside phosphate biosynthetic process | 61/3246 | 256/18723 | 4.84e-03 | 2.37e-02 | 61 |
GO:000912612 | Prostate | Tumor | purine nucleoside monophosphate metabolic process | 15/3246 | 44/18723 | 5.49e-03 | 2.61e-02 | 15 |
GO:00091676 | Prostate | Tumor | purine ribonucleoside monophosphate metabolic process | 14/3246 | 41/18723 | 7.07e-03 | 3.18e-02 | 14 |
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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 |
AMPD1 | SNV | Missense_Mutation | rs149424604 | c.686N>A | p.Arg229Gln | p.R229Q | P23109 | protein_coding | tolerated(0.49) | benign(0.001) | TCGA-DD-AADR-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
AMPD1 | SNV | Missense_Mutation | c.878N>T | p.Thr293Ile | p.T293I | P23109 | protein_coding | deleterious(0) | benign(0.097) | TCGA-DD-AAW3-01 | Liver | liver hepatocellular carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
AMPD1 | SNV | Missense_Mutation | c.1691N>T | p.Gln564Leu | p.Q564L | P23109 | protein_coding | deleterious(0.03) | benign(0.284) | TCGA-UB-A7MB-01 | Liver | liver hepatocellular carcinoma | Male | <65 | I/II | Targeted Molecular therapy | sorafenib | PD | |
AMPD1 | SNV | Missense_Mutation | rs144014236 | c.1320C>G | p.Ile440Met | p.I440M | P23109 | protein_coding | deleterious(0.02) | probably_damaging(0.972) | TCGA-05-4398-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | CR |
AMPD1 | SNV | Missense_Mutation | c.781N>A | p.Glu261Lys | p.E261K | P23109 | protein_coding | tolerated(0.4) | benign(0.005) | TCGA-44-2665-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Targeted Molecular therapy | bevacizumab | SD | |
AMPD1 | SNV | Missense_Mutation | c.802N>A | p.Pro268Thr | p.P268T | P23109 | protein_coding | deleterious(0.01) | possibly_damaging(0.713) | TCGA-55-A490-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | SD | |
AMPD1 | SNV | Missense_Mutation | rs752158310 | c.748N>A | p.Val250Ile | p.V250I | P23109 | protein_coding | tolerated(0.21) | benign(0.003) | TCGA-55-A494-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
AMPD1 | SNV | Missense_Mutation | c.361C>A | p.Leu121Ile | p.L121I | P23109 | protein_coding | tolerated(0.44) | benign(0) | TCGA-55-A4DG-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
AMPD1 | SNV | Missense_Mutation | c.278N>C | p.His93Pro | p.H93P | P23109 | protein_coding | tolerated(0.1) | benign(0.071) | TCGA-64-1678-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | SD | |
AMPD1 | SNV | Missense_Mutation | novel | c.2170G>A | p.Gly724Arg | p.G724R | P23109 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-69-7974-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | 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 |
270 | AMPD1 | DRUGGABLE GENOME, ENZYME | methotrexate | METHOTREXATE | 20386493,27217051,29520081,16947783,27992285 | |
270 | AMPD1 | DRUGGABLE GENOME, ENZYME | regadenoson | REGADENOSON | 26554440 |
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