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Gene: CPS1 |
Gene summary for CPS1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | CPS1 | Gene ID | 1373 |
| Gene name | carbamoyl-phosphate synthase 1 | |
| Gene Alias | CPSASE1 | |
| Cytomap | 2q34 | |
| Gene Type | protein-coding | GO ID | GO:0000050 | UniProtAcc | P31327 |
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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 |
| 1373 | CPS1 | NAFLD1 | Human | Liver | NAFLD | 6.52e-14 | 1.39e+00 | -0.04 |
| 1373 | CPS1 | S41 | Human | Liver | Cirrhotic | 5.18e-09 | 1.11e+00 | -0.0343 |
| 1373 | CPS1 | S44 | Human | Liver | HCC | 1.02e-12 | 1.48e+00 | -0.0083 |
| 1373 | CPS1 | HCC1_Meng | Human | Liver | HCC | 1.76e-21 | -6.12e-01 | 0.0246 |
| 1373 | CPS1 | HCC2_Meng | Human | Liver | HCC | 3.58e-14 | -6.22e-01 | 0.0107 |
| 1373 | CPS1 | cirrhotic1 | Human | Liver | Cirrhotic | 9.67e-14 | -6.04e-01 | 0.0202 |
| 1373 | CPS1 | cirrhotic2 | Human | Liver | Cirrhotic | 2.29e-16 | -5.58e-01 | 0.0201 |
| 1373 | CPS1 | cirrhotic3 | Human | Liver | Cirrhotic | 7.62e-07 | -5.96e-01 | 0.0215 |
| 1373 | CPS1 | HCC1 | Human | Liver | HCC | 1.24e-10 | -3.63e-01 | 0.5336 |
| 1373 | CPS1 | HCC2 | Human | Liver | HCC | 4.55e-16 | 3.70e+00 | 0.5341 |
| 1373 | CPS1 | Pt13.a | Human | Liver | HCC | 4.18e-28 | -3.18e-01 | 0.021 |
| 1373 | CPS1 | Pt13.b | Human | Liver | HCC | 6.88e-31 | -3.15e-01 | 0.0251 |
| 1373 | CPS1 | Pt14.b | Human | Liver | HCC | 3.86e-14 | 4.27e-02 | 0.018 |
| 1373 | CPS1 | Pt14.d | Human | Liver | HCC | 2.91e-16 | -4.64e-01 | 0.0143 |
| 1373 | CPS1 | S014 | Human | Liver | HCC | 6.89e-05 | -5.15e-01 | 0.2254 |
| 1373 | CPS1 | S016 | Human | Liver | HCC | 9.10e-06 | -6.17e-01 | 0.2243 |
| 1373 | CPS1 | S028 | Human | Liver | HCC | 3.24e-02 | -5.85e-01 | 0.2503 |
| 1373 | CPS1 | S029 | Human | Liver | HCC | 9.37e-03 | -6.23e-01 | 0.2581 |
| 1373 | CPS1 | Pat01-B | Human | Stomach | GC | 1.57e-15 | 3.35e-01 | 0.5754 |
| 1373 | CPS1 | Pat02-B | Human | Stomach | GC | 8.23e-12 | 2.74e-01 | 0.0368 |
| Page: 1 2 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:00160535 | Liver | NAFLD | organic acid biosynthetic process | 77/1882 | 316/18723 | 1.03e-13 | 6.69e-11 | 77 |
| GO:00463945 | Liver | NAFLD | carboxylic acid biosynthetic process | 75/1882 | 314/18723 | 6.37e-13 | 3.39e-10 | 75 |
| GO:00485457 | Liver | NAFLD | response to steroid hormone | 75/1882 | 339/18723 | 3.44e-11 | 1.12e-08 | 75 |
| GO:00713755 | Liver | NAFLD | cellular response to peptide hormone stimulus | 65/1882 | 290/18723 | 3.95e-10 | 9.62e-08 | 65 |
| GO:00065203 | Liver | NAFLD | cellular amino acid metabolic process | 63/1882 | 284/18723 | 1.14e-09 | 2.17e-07 | 63 |
| GO:00442425 | Liver | NAFLD | cellular lipid catabolic process | 52/1882 | 214/18723 | 1.15e-09 | 2.17e-07 | 52 |
| GO:00094107 | Liver | NAFLD | response to xenobiotic stimulus | 88/1882 | 462/18723 | 2.53e-09 | 4.11e-07 | 88 |
| GO:00086523 | Liver | NAFLD | cellular amino acid biosynthetic process | 26/1882 | 76/18723 | 1.00e-08 | 1.33e-06 | 26 |
| GO:19016536 | Liver | NAFLD | cellular response to peptide | 71/1882 | 359/18723 | 1.82e-08 | 2.09e-06 | 71 |
| GO:19016053 | Liver | NAFLD | alpha-amino acid metabolic process | 46/1882 | 195/18723 | 2.74e-08 | 2.86e-06 | 46 |
| GO:00610087 | Liver | NAFLD | hepaticobiliary system development | 38/1882 | 150/18723 | 5.94e-08 | 5.42e-06 | 38 |
| GO:00316677 | Liver | NAFLD | response to nutrient levels | 85/1882 | 474/18723 | 8.23e-08 | 7.09e-06 | 85 |
| GO:00066413 | Liver | NAFLD | triglyceride metabolic process | 29/1882 | 100/18723 | 9.51e-08 | 7.62e-06 | 29 |
| GO:00018897 | Liver | NAFLD | liver development | 37/1882 | 147/18723 | 1.06e-07 | 8.12e-06 | 37 |
| GO:00160426 | Liver | NAFLD | lipid catabolic process | 63/1882 | 320/18723 | 1.35e-07 | 1.02e-05 | 63 |
| GO:00434346 | Liver | NAFLD | response to peptide hormone | 76/1882 | 414/18723 | 1.51e-07 | 1.09e-05 | 76 |
| GO:00513846 | Liver | NAFLD | response to glucocorticoid | 36/1882 | 148/18723 | 3.88e-07 | 2.52e-05 | 36 |
| GO:19016073 | Liver | NAFLD | alpha-amino acid biosynthetic process | 22/1882 | 68/18723 | 4.13e-07 | 2.62e-05 | 22 |
| GO:00066392 | Liver | NAFLD | acylglycerol metabolic process | 32/1882 | 128/18723 | 8.82e-07 | 4.60e-05 | 32 |
| GO:00066382 | Liver | NAFLD | neutral lipid metabolic process | 32/1882 | 129/18723 | 1.06e-06 | 5.35e-05 | 32 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0120010 | Liver | NAFLD | Carbon metabolism | 26/1043 | 115/8465 | 1.39e-03 | 1.71e-02 | 1.38e-02 | 26 |
| hsa0120011 | Liver | NAFLD | Carbon metabolism | 26/1043 | 115/8465 | 1.39e-03 | 1.71e-02 | 1.38e-02 | 26 |
| hsa0120021 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
| hsa012304 | Liver | Cirrhotic | Biosynthesis of amino acids | 35/2530 | 75/8465 | 1.54e-03 | 7.83e-03 | 4.83e-03 | 35 |
| hsa0120031 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
| hsa0123011 | Liver | Cirrhotic | Biosynthesis of amino acids | 35/2530 | 75/8465 | 1.54e-03 | 7.83e-03 | 4.83e-03 | 35 |
| hsa0120041 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
| hsa0123021 | Liver | HCC | Biosynthesis of amino acids | 53/4020 | 75/8465 | 3.79e-05 | 2.11e-04 | 1.18e-04 | 53 |
| hsa0120051 | Liver | HCC | Carbon metabolism | 89/4020 | 115/8465 | 3.92e-11 | 6.56e-10 | 3.65e-10 | 89 |
| hsa0123031 | Liver | HCC | Biosynthesis of amino acids | 53/4020 | 75/8465 | 3.79e-05 | 2.11e-04 | 1.18e-04 | 53 |
| hsa00220 | Stomach | GC | Arginine biosynthesis | 6/708 | 22/8465 | 7.81e-03 | 4.10e-02 | 2.88e-02 | 6 |
| hsa002201 | Stomach | GC | Arginine biosynthesis | 6/708 | 22/8465 | 7.81e-03 | 4.10e-02 | 2.88e-02 | 6 |
| hsa00910 | Stomach | SIM | Nitrogen metabolism | 5/465 | 17/8465 | 1.75e-03 | 1.33e-02 | 1.07e-02 | 5 |
| hsa009101 | Stomach | SIM | Nitrogen metabolism | 5/465 | 17/8465 | 1.75e-03 | 1.33e-02 | 1.07e-02 | 5 |
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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. |
| 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 |
| CPS1 | SNV | Missense_Mutation | novel | c.3547G>C | p.Glu1183Gln | p.E1183Q | P31327 | protein_coding | deleterious(0) | probably_damaging(0.967) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
| CPS1 | SNV | Missense_Mutation | novel | c.1277N>C | p.Val426Ala | p.V426A | P31327 | protein_coding | tolerated(0.45) | benign(0.001) | TCGA-A2-A0CW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD |
| CPS1 | SNV | Missense_Mutation | novel | c.2698N>G | p.Leu900Val | p.L900V | P31327 | protein_coding | tolerated(0.22) | benign(0.005) | TCGA-A7-A4SE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| CPS1 | SNV | Missense_Mutation | c.1212N>G | p.Ile404Met | p.I404M | P31327 | protein_coding | tolerated(0.06) | benign(0.054) | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| CPS1 | SNV | Missense_Mutation | c.3843N>A | p.Phe1281Leu | p.F1281L | P31327 | protein_coding | tolerated(0.57) | benign(0.306) | TCGA-A8-A08F-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR | |
| CPS1 | SNV | Missense_Mutation | c.2039A>T | p.Asn680Ile | p.N680I | P31327 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-A8-A09D-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR | |
| CPS1 | SNV | Missense_Mutation | c.3166N>A | p.Gly1056Ser | p.G1056S | P31327 | protein_coding | tolerated(0.99) | benign(0) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| CPS1 | SNV | Missense_Mutation | rs376091629 | c.581N>G | p.Gln194Arg | p.Q194R | P31327 | protein_coding | tolerated(0.17) | benign(0.014) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CPS1 | SNV | Missense_Mutation | rs774692248 | c.3655C>A | p.Gln1219Lys | p.Q1219K | P31327 | protein_coding | deleterious(0) | possibly_damaging(0.571) | TCGA-B6-A40B-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| CPS1 | SNV | Missense_Mutation | novel | c.1760N>A | p.Gly587Asp | p.G587D | P31327 | protein_coding | deleterious(0) | possibly_damaging(0.764) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 |
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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 |
| 1373 | CPS1 | CLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOME | sodium phenylbutyrate | |||
| 1373 | CPS1 | CLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOME | Polidocanol - BioForm Medical/Chemische Fabrik Kreussler & Co | |||
| 1373 | CPS1 | CLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOME | positive modulator | CHEMBL1201780 | CARGLUMIC ACID | |
| 1373 | CPS1 | CLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOME | sodium benzoate / sodium phenylacetate | |||
| 1373 | CPS1 | CLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOME | l-methionine | METHIONINE | 24651765 | |
| 1373 | CPS1 | CLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOME | valproic acid | 20456087 | ||
| 1373 | CPS1 | CLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOME | Sodium Phenylbutyrate | |||
| 1373 | CPS1 | CLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOME | Carglumic acid | |||
| 1373 | CPS1 | CLINICALLY ACTIONABLE, ENZYME, DRUGGABLE GENOME | antiepileptics | 20456087 |
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