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Gene: AMPD2 |
Gene summary for AMPD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | AMPD2 | Gene ID | 271 |
| Gene name | adenosine monophosphate deaminase 2 | |
| Gene Alias | PCH9 | |
| Cytomap | 1p13.3 | |
| Gene Type | protein-coding | GO ID | GO:0006139 | UniProtAcc | A0A024R098 |
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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 |
| 271 | AMPD2 | HCC1_Meng | Human | Liver | HCC | 5.27e-28 | 4.25e-02 | 0.0246 |
| 271 | AMPD2 | HCC2_Meng | Human | Liver | HCC | 1.75e-08 | 8.22e-02 | 0.0107 |
| 271 | AMPD2 | HCC2 | Human | Liver | HCC | 4.52e-22 | 3.61e+00 | 0.5341 |
| 271 | AMPD2 | S014 | Human | Liver | HCC | 8.41e-13 | 3.62e-01 | 0.2254 |
| 271 | AMPD2 | S015 | Human | Liver | HCC | 3.64e-17 | 6.04e-01 | 0.2375 |
| 271 | AMPD2 | S016 | Human | Liver | HCC | 3.05e-13 | 4.05e-01 | 0.2243 |
| 271 | AMPD2 | S027 | Human | Liver | HCC | 3.86e-13 | 7.07e-01 | 0.2446 |
| 271 | AMPD2 | S028 | Human | Liver | HCC | 3.65e-22 | 7.60e-01 | 0.2503 |
| 271 | AMPD2 | S029 | Human | Liver | HCC | 1.87e-22 | 8.27e-01 | 0.2581 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease |
| ∗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:000911722 | Liver | HCC | nucleotide metabolic process | 300/7958 | 489/18723 | 1.61e-17 | 1.71e-15 | 300 |
| GO:000675322 | Liver | HCC | nucleoside phosphate metabolic process | 304/7958 | 497/18723 | 1.78e-17 | 1.85e-15 | 304 |
| GO:001969322 | Liver | HCC | ribose phosphate metabolic process | 248/7958 | 396/18723 | 3.15e-16 | 2.70e-14 | 248 |
| GO:000925922 | Liver | HCC | ribonucleotide metabolic process | 240/7958 | 385/18723 | 2.07e-15 | 1.51e-13 | 240 |
| GO:000915022 | Liver | HCC | purine ribonucleotide metabolic process | 226/7958 | 368/18723 | 1.36e-13 | 7.69e-12 | 226 |
| GO:007252122 | Liver | HCC | purine-containing compound metabolic process | 250/7958 | 416/18723 | 2.26e-13 | 1.24e-11 | 250 |
| GO:000616322 | Liver | HCC | purine nucleotide metabolic process | 236/7958 | 396/18723 | 3.59e-12 | 1.62e-10 | 236 |
| GO:000916512 | Liver | HCC | nucleotide biosynthetic process | 150/7958 | 254/18723 | 6.79e-08 | 1.40e-06 | 150 |
| GO:190129312 | Liver | HCC | nucleoside phosphate biosynthetic process | 151/7958 | 256/18723 | 6.84e-08 | 1.41e-06 | 151 |
| GO:004639012 | Liver | HCC | ribose phosphate biosynthetic process | 116/7958 | 190/18723 | 1.79e-07 | 3.29e-06 | 116 |
| GO:000926012 | Liver | HCC | ribonucleotide biosynthetic process | 111/7958 | 182/18723 | 3.53e-07 | 6.03e-06 | 111 |
| GO:000915212 | Liver | HCC | purine ribonucleotide biosynthetic process | 101/7958 | 169/18723 | 4.30e-06 | 5.50e-05 | 101 |
| GO:000912311 | Liver | HCC | nucleoside monophosphate metabolic process | 52/7958 | 76/18723 | 4.35e-06 | 5.54e-05 | 52 |
| GO:00091612 | Liver | HCC | ribonucleoside monophosphate metabolic process | 41/7958 | 58/18723 | 1.29e-05 | 1.44e-04 | 41 |
| GO:007252212 | Liver | HCC | purine-containing compound biosynthetic process | 114/7958 | 200/18723 | 2.36e-05 | 2.49e-04 | 114 |
| GO:000616412 | Liver | HCC | purine nucleotide biosynthetic process | 107/7958 | 191/18723 | 1.08e-04 | 9.22e-04 | 107 |
| GO:0043094 | Liver | HCC | cellular metabolic compound salvage | 20/7958 | 26/18723 | 3.82e-04 | 2.61e-03 | 20 |
| GO:00091241 | Liver | HCC | nucleoside monophosphate biosynthetic process | 29/7958 | 42/18723 | 4.57e-04 | 3.04e-03 | 29 |
| GO:000912611 | Liver | HCC | purine nucleoside monophosphate metabolic process | 30/7958 | 44/18723 | 5.12e-04 | 3.33e-03 | 30 |
| GO:000916711 | Liver | HCC | purine ribonucleoside monophosphate metabolic process | 28/7958 | 41/18723 | 7.54e-04 | 4.55e-03 | 28 |
| Page: 1 2 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa012322 | Liver | HCC | Nucleotide metabolism | 59/4020 | 85/8465 | 3.30e-05 | 1.88e-04 | 1.04e-04 | 59 |
| hsa012323 | Liver | HCC | Nucleotide metabolism | 59/4020 | 85/8465 | 3.30e-05 | 1.88e-04 | 1.04e-04 | 59 |
| Page: 1 |
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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 |
| Page: 1 |
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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 |
| AMPD2 | SNV | Missense_Mutation | novel | c.662N>A | p.Arg221Gln | p.R221Q | Q01433 | protein_coding | deleterious(0.01) | benign(0.434) | TCGA-C8-A132-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| AMPD2 | SNV | Missense_Mutation | rs781032788 | c.397C>T | p.Arg133Cys | p.R133C | Q01433 | protein_coding | deleterious(0.02) | possibly_damaging(0.858) | TCGA-E9-A228-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
| AMPD2 | SNV | Missense_Mutation | rs776868175 | c.1132C>T | p.Arg378Trp | p.R378W | Q01433 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| AMPD2 | SNV | Missense_Mutation | novel | c.1436C>T | p.Ala479Val | p.A479V | Q01433 | protein_coding | deleterious(0) | possibly_damaging(0.695) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| AMPD2 | SNV | Missense_Mutation | rs764075553 | c.800G>A | p.Arg267His | p.R267H | Q01433 | protein_coding | deleterious(0.03) | benign(0.411) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| AMPD2 | SNV | Missense_Mutation | c.2320G>C | p.Glu774Gln | p.E774Q | Q01433 | protein_coding | deleterious(0) | probably_damaging(0.92) | TCGA-EK-A2PG-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| AMPD2 | SNV | Missense_Mutation | rs774595273 | c.1675N>A | p.Val559Ile | p.V559I | Q01433 | protein_coding | tolerated(0.6) | benign(0.03) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
| AMPD2 | SNV | Missense_Mutation | c.1310N>A | p.Ala437Glu | p.A437E | Q01433 | protein_coding | tolerated(0.13) | benign(0.216) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| AMPD2 | SNV | Missense_Mutation | c.2159N>G | p.Gln720Arg | p.Q720R | Q01433 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3663-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| AMPD2 | SNV | Missense_Mutation | c.2141N>A | p.Arg714His | p.R714H | Q01433 | protein_coding | deleterious(0) | possibly_damaging(0.591) | TCGA-AA-3715-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
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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 |
| Page: 1 |
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