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Gene: PRODH2 |
Gene summary for PRODH2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PRODH2 | Gene ID | 58510 |
| Gene name | proline dehydrogenase 2 | |
| Gene Alias | HSPOX1 | |
| Cytomap | 19q13.12 | |
| Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | Q9UF12 |
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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 |
| 58510 | PRODH2 | S43 | Human | Liver | Cirrhotic | 1.07e-02 | -5.46e-02 | -0.0187 |
| 58510 | PRODH2 | HCC1_Meng | Human | Liver | HCC | 1.86e-74 | 4.17e-01 | 0.0246 |
| 58510 | PRODH2 | HCC2_Meng | Human | Liver | HCC | 9.14e-03 | -9.37e-02 | 0.0107 |
| 58510 | PRODH2 | cirrhotic1 | Human | Liver | Cirrhotic | 9.68e-04 | -6.90e-02 | 0.0202 |
| 58510 | PRODH2 | HCC1 | Human | Liver | HCC | 1.67e-11 | 3.30e+00 | 0.5336 |
| 58510 | PRODH2 | HCC2 | Human | Liver | HCC | 1.91e-18 | 3.45e+00 | 0.5341 |
| 58510 | PRODH2 | S014 | Human | Liver | HCC | 1.68e-15 | 7.57e-01 | 0.2254 |
| 58510 | PRODH2 | S015 | Human | Liver | HCC | 3.09e-27 | 1.80e+00 | 0.2375 |
| 58510 | PRODH2 | S016 | Human | Liver | HCC | 1.85e-22 | 9.18e-01 | 0.2243 |
| 58510 | PRODH2 | S028 | Human | Liver | HCC | 3.90e-09 | 5.20e-01 | 0.2503 |
| 58510 | PRODH2 | S029 | Human | Liver | HCC | 3.29e-19 | 9.50e-01 | 0.2581 |
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| 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:004428211 | Liver | Cirrhotic | small molecule catabolic process | 151/4634 | 376/18723 | 2.20e-11 | 1.34e-09 | 151 |
| GO:001605411 | Liver | Cirrhotic | organic acid catabolic process | 104/4634 | 240/18723 | 1.91e-10 | 9.53e-09 | 104 |
| GO:004639511 | Liver | Cirrhotic | carboxylic acid catabolic process | 102/4634 | 236/18723 | 3.41e-10 | 1.63e-08 | 102 |
| GO:19016051 | Liver | Cirrhotic | alpha-amino acid metabolic process | 82/4634 | 195/18723 | 7.72e-08 | 2.30e-06 | 82 |
| GO:00090631 | Liver | Cirrhotic | cellular amino acid catabolic process | 49/4634 | 110/18723 | 4.47e-06 | 7.42e-05 | 49 |
| GO:000652011 | Liver | Cirrhotic | cellular amino acid metabolic process | 103/4634 | 284/18723 | 8.88e-06 | 1.30e-04 | 103 |
| GO:004364811 | Liver | Cirrhotic | dicarboxylic acid metabolic process | 43/4634 | 96/18723 | 1.42e-05 | 1.97e-04 | 43 |
| GO:19016061 | Liver | Cirrhotic | alpha-amino acid catabolic process | 36/4634 | 87/18723 | 4.69e-04 | 3.78e-03 | 36 |
| GO:004428221 | Liver | HCC | small molecule catabolic process | 225/7958 | 376/18723 | 6.50e-12 | 2.80e-10 | 225 |
| GO:001605421 | Liver | HCC | organic acid catabolic process | 152/7958 | 240/18723 | 5.11e-11 | 1.92e-09 | 152 |
| GO:00463952 | Liver | HCC | carboxylic acid catabolic process | 149/7958 | 236/18723 | 1.11e-10 | 3.87e-09 | 149 |
| GO:19016052 | Liver | HCC | alpha-amino acid metabolic process | 124/7958 | 195/18723 | 2.07e-09 | 5.79e-08 | 124 |
| GO:00436482 | Liver | HCC | dicarboxylic acid metabolic process | 68/7958 | 96/18723 | 1.73e-08 | 4.14e-07 | 68 |
| GO:00065202 | Liver | HCC | cellular amino acid metabolic process | 167/7958 | 284/18723 | 1.91e-08 | 4.56e-07 | 167 |
| GO:00090632 | Liver | HCC | cellular amino acid catabolic process | 70/7958 | 110/18723 | 6.12e-06 | 7.52e-05 | 70 |
| GO:19016062 | Liver | HCC | alpha-amino acid catabolic process | 53/7958 | 87/18723 | 4.01e-04 | 2.71e-03 | 53 |
| GO:0009064 | Liver | HCC | glutamine family amino acid metabolic process | 47/7958 | 78/18723 | 1.17e-03 | 6.54e-03 | 47 |
| GO:0006536 | Liver | HCC | glutamate metabolic process | 21/7958 | 33/18723 | 1.16e-02 | 4.28e-02 | 21 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa003308 | Liver | Cirrhotic | Arginine and proline metabolism | 25/2530 | 50/8465 | 2.18e-03 | 9.41e-03 | 5.80e-03 | 25 |
| hsa0033011 | Liver | Cirrhotic | Arginine and proline metabolism | 25/2530 | 50/8465 | 2.18e-03 | 9.41e-03 | 5.80e-03 | 25 |
| hsa0033021 | Liver | HCC | Arginine and proline metabolism | 33/4020 | 50/8465 | 6.28e-03 | 1.77e-02 | 9.83e-03 | 33 |
| hsa0033031 | Liver | HCC | Arginine and proline metabolism | 33/4020 | 50/8465 | 6.28e-03 | 1.77e-02 | 9.83e-03 | 33 |
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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 |
| PRODH2 | SNV | Missense_Mutation | c.1493N>C | p.Leu498Pro | p.L498P | Q9UF12 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-BH-A18G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PRODH2 | SNV | Missense_Mutation | novel | c.1050N>T | p.Gln350His | p.Q350H | Q9UF12 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| PRODH2 | SNV | Missense_Mutation | rs145296462 | c.257N>G | p.Ser86Cys | p.S86C | Q9UF12 | protein_coding | deleterious_low_confidence(0.05) | possibly_damaging(0.781) | TCGA-E2-A14N-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
| PRODH2 | SNV | Missense_Mutation | novel | c.13N>C | p.Val5Leu | p.V5L | Q9UF12 | protein_coding | benign(0) | TCGA-DS-A1OD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| PRODH2 | SNV | Missense_Mutation | rs370209287 | c.236N>A | p.Arg79Gln | p.R79Q | Q9UF12 | protein_coding | tolerated_low_confidence(0.24) | benign(0) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PRODH2 | SNV | Missense_Mutation | rs780775017 | c.655C>T | p.Arg219Trp | p.R219W | Q9UF12 | protein_coding | deleterious(0) | benign(0.424) | TCGA-VS-A9UI-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
| PRODH2 | SNV | Missense_Mutation | c.131N>A | p.Cys44Tyr | p.C44Y | Q9UF12 | protein_coding | tolerated_low_confidence(0.12) | benign(0) | TCGA-A6-6781-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | SD | |
| PRODH2 | SNV | Missense_Mutation | c.48N>G | p.Ser16Arg | p.S16R | Q9UF12 | protein_coding | benign(0.007) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
| PRODH2 | SNV | Missense_Mutation | novel | c.94N>C | p.Asn32His | p.N32H | Q9UF12 | protein_coding | tolerated_low_confidence(0.09) | benign(0.094) | TCGA-AZ-4315-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PRODH2 | SNV | Missense_Mutation | rs182628111 | c.1013N>T | p.Pro338Leu | p.P338L | Q9UF12 | protein_coding | deleterious(0.03) | benign(0.146) | TCGA-AZ-6600-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | cpt-11 | 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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