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Gene: PYCR2 |
Gene summary for PYCR2 |
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Gene information | Species | Human | Gene symbol | PYCR2 | Gene ID | 29920 |
Gene name | pyrroline-5-carboxylate reductase 2 | |
Gene Alias | HLD10 | |
Cytomap | 1q42.12 | |
Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | A0A087WTV6 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
29920 | PYCR2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.29e-05 | 1.54e-01 | 0.0155 |
29920 | PYCR2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.37e-03 | 1.71e-01 | -0.1808 |
29920 | PYCR2 | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.40e-03 | 2.22e-01 | 0.0216 |
29920 | PYCR2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 8.45e-11 | 3.82e-01 | -0.0811 |
29920 | PYCR2 | HTA11_78_2000001011 | Human | Colorectum | AD | 8.26e-09 | 2.42e-01 | -0.1088 |
29920 | PYCR2 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.51e-09 | 2.09e-01 | -0.1954 |
29920 | PYCR2 | HTA11_411_2000001011 | Human | Colorectum | SER | 5.61e-03 | 2.55e-01 | -0.2602 |
29920 | PYCR2 | HTA11_3361_2000001011 | Human | Colorectum | AD | 2.57e-07 | 2.67e-01 | -0.1207 |
29920 | PYCR2 | HTA11_83_2000001011 | Human | Colorectum | SER | 1.79e-04 | 1.91e-01 | -0.1526 |
29920 | PYCR2 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.96e-10 | 2.47e-01 | -0.1464 |
29920 | PYCR2 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.07e-07 | 1.85e-01 | -0.1001 |
29920 | PYCR2 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.53e-17 | 3.66e-01 | -0.059 |
29920 | PYCR2 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.72e-05 | 2.63e-01 | -0.1706 |
29920 | PYCR2 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.28e-02 | 1.70e-01 | -0.2061 |
29920 | PYCR2 | HTA11_5216_2000001011 | Human | Colorectum | SER | 3.40e-02 | 2.52e-01 | -0.1462 |
29920 | PYCR2 | HTA11_546_2000001011 | Human | Colorectum | AD | 7.78e-03 | 1.68e-01 | -0.0842 |
29920 | PYCR2 | HTA11_7862_2000001011 | Human | Colorectum | AD | 1.12e-06 | 2.52e-01 | -0.0179 |
29920 | PYCR2 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.60e-16 | 3.65e-01 | 0.096 |
29920 | PYCR2 | HTA11_4255_2000001011 | Human | Colorectum | SER | 3.40e-03 | 2.22e-01 | 0.0446 |
29920 | PYCR2 | HTA11_8622_2000001021 | Human | Colorectum | SER | 8.37e-05 | 2.67e-01 | 0.0528 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0006979 | Colorectum | AD | response to oxidative stress | 145/3918 | 446/18723 | 5.16e-09 | 3.23e-07 | 145 |
GO:0062197 | Colorectum | AD | cellular response to chemical stress | 109/3918 | 337/18723 | 5.33e-07 | 1.95e-05 | 109 |
GO:0034599 | Colorectum | AD | cellular response to oxidative stress | 94/3918 | 288/18723 | 2.03e-06 | 6.02e-05 | 94 |
GO:0006520 | Colorectum | AD | cellular amino acid metabolic process | 81/3918 | 284/18723 | 1.37e-03 | 1.19e-02 | 81 |
GO:00069791 | Colorectum | SER | response to oxidative stress | 114/2897 | 446/18723 | 1.75e-08 | 1.28e-06 | 114 |
GO:00621971 | Colorectum | SER | cellular response to chemical stress | 87/2897 | 337/18723 | 5.33e-07 | 2.59e-05 | 87 |
GO:00345991 | Colorectum | SER | cellular response to oxidative stress | 73/2897 | 288/18723 | 8.52e-06 | 2.86e-04 | 73 |
GO:00065201 | Colorectum | SER | cellular amino acid metabolic process | 61/2897 | 284/18723 | 4.20e-03 | 3.41e-02 | 61 |
GO:00069792 | Colorectum | MSS | response to oxidative stress | 128/3467 | 446/18723 | 7.65e-08 | 3.81e-06 | 128 |
GO:00621972 | Colorectum | MSS | cellular response to chemical stress | 102/3467 | 337/18723 | 9.73e-08 | 4.71e-06 | 102 |
GO:00345992 | Colorectum | MSS | cellular response to oxidative stress | 88/3467 | 288/18723 | 4.58e-07 | 1.77e-05 | 88 |
GO:0046394 | Colorectum | MSS | carboxylic acid biosynthetic process | 76/3467 | 314/18723 | 6.71e-03 | 4.38e-02 | 76 |
GO:0016053 | Colorectum | MSS | organic acid biosynthetic process | 76/3467 | 316/18723 | 7.88e-03 | 4.84e-02 | 76 |
GO:00069793 | Colorectum | MSI-H | response to oxidative stress | 68/1319 | 446/18723 | 1.17e-09 | 1.59e-07 | 68 |
GO:00621973 | Colorectum | MSI-H | cellular response to chemical stress | 51/1319 | 337/18723 | 1.78e-07 | 1.52e-05 | 51 |
GO:00345993 | Colorectum | MSI-H | cellular response to oxidative stress | 43/1319 | 288/18723 | 2.31e-06 | 1.40e-04 | 43 |
GO:1901605 | Colorectum | MSI-H | alpha-amino acid metabolic process | 26/1319 | 195/18723 | 1.26e-03 | 2.02e-02 | 26 |
GO:0008652 | Colorectum | MSI-H | cellular amino acid biosynthetic process | 13/1319 | 76/18723 | 2.35e-03 | 3.12e-02 | 13 |
GO:1901607 | Colorectum | MSI-H | alpha-amino acid biosynthetic process | 12/1319 | 68/18723 | 2.60e-03 | 3.41e-02 | 12 |
GO:00463941 | Colorectum | MSI-H | carboxylic acid biosynthetic process | 36/1319 | 314/18723 | 2.68e-03 | 3.48e-02 | 36 |
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Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa00330 | Colorectum | AD | Arginine and proline metabolism | 23/2092 | 50/8465 | 8.27e-04 | 5.90e-03 | 3.76e-03 | 23 |
hsa01230 | Colorectum | AD | Biosynthesis of amino acids | 28/2092 | 75/8465 | 9.99e-03 | 3.89e-02 | 2.48e-02 | 28 |
hsa003301 | Colorectum | AD | Arginine and proline metabolism | 23/2092 | 50/8465 | 8.27e-04 | 5.90e-03 | 3.76e-03 | 23 |
hsa012301 | Colorectum | AD | Biosynthesis of amino acids | 28/2092 | 75/8465 | 9.99e-03 | 3.89e-02 | 2.48e-02 | 28 |
hsa003302 | Colorectum | SER | Arginine and proline metabolism | 17/1580 | 50/8465 | 7.12e-03 | 3.77e-02 | 2.74e-02 | 17 |
hsa012302 | Colorectum | SER | Biosynthesis of amino acids | 23/1580 | 75/8465 | 8.11e-03 | 4.14e-02 | 3.01e-02 | 23 |
hsa003303 | Colorectum | SER | Arginine and proline metabolism | 17/1580 | 50/8465 | 7.12e-03 | 3.77e-02 | 2.74e-02 | 17 |
hsa012303 | Colorectum | SER | Biosynthesis of amino acids | 23/1580 | 75/8465 | 8.11e-03 | 4.14e-02 | 3.01e-02 | 23 |
hsa003304 | Colorectum | MSS | Arginine and proline metabolism | 23/1875 | 50/8465 | 1.52e-04 | 1.24e-03 | 7.61e-04 | 23 |
hsa003305 | Colorectum | MSS | Arginine and proline metabolism | 23/1875 | 50/8465 | 1.52e-04 | 1.24e-03 | 7.61e-04 | 23 |
hsa012306 | Esophagus | HGIN | Biosynthesis of amino acids | 21/1383 | 75/8465 | 7.38e-03 | 4.63e-02 | 3.68e-02 | 21 |
hsa0123013 | Esophagus | HGIN | Biosynthesis of amino acids | 21/1383 | 75/8465 | 7.38e-03 | 4.63e-02 | 3.68e-02 | 21 |
hsa0123023 | Esophagus | ESCC | Biosynthesis of amino acids | 49/4205 | 75/8465 | 4.35e-03 | 1.12e-02 | 5.74e-03 | 49 |
hsa0123033 | Esophagus | ESCC | Biosynthesis of amino acids | 49/4205 | 75/8465 | 4.35e-03 | 1.12e-02 | 5.74e-03 | 49 |
hsa012304 | Liver | Cirrhotic | Biosynthesis of amino acids | 35/2530 | 75/8465 | 1.54e-03 | 7.83e-03 | 4.83e-03 | 35 |
hsa003308 | Liver | Cirrhotic | Arginine and proline metabolism | 25/2530 | 50/8465 | 2.18e-03 | 9.41e-03 | 5.80e-03 | 25 |
hsa0123011 | Liver | Cirrhotic | Biosynthesis of amino acids | 35/2530 | 75/8465 | 1.54e-03 | 7.83e-03 | 4.83e-03 | 35 |
hsa0033011 | Liver | Cirrhotic | Arginine and proline metabolism | 25/2530 | 50/8465 | 2.18e-03 | 9.41e-03 | 5.80e-03 | 25 |
hsa0123021 | Liver | HCC | Biosynthesis of amino acids | 53/4020 | 75/8465 | 3.79e-05 | 2.11e-04 | 1.18e-04 | 53 |
hsa0033021 | 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 |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
PYCR2 | SNV | Missense_Mutation | c.184N>A | p.His62Asn | p.H62N | Q96C36 | protein_coding | tolerated(0.68) | benign(0.005) | TCGA-50-5051-01 | Lung | lung adenocarcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | PD | |
PYCR2 | SNV | Missense_Mutation | c.441N>T | p.Gln147His | p.Q147H | Q96C36 | protein_coding | tolerated(0.09) | benign(0.139) | TCGA-55-6979-01 | Lung | lung adenocarcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | PD | |
PYCR2 | SNV | Missense_Mutation | c.363N>T | p.Met121Ile | p.M121I | Q96C36 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-86-8073-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
PYCR2 | SNV | Missense_Mutation | novel | c.457N>T | p.Met153Leu | p.M153L | Q96C36 | protein_coding | tolerated(1) | benign(0.001) | TCGA-NJ-A4YQ-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PYCR2 | SNV | Missense_Mutation | rs375432992 | c.256G>A | p.Val86Met | p.V86M | Q96C36 | protein_coding | deleterious(0.02) | possibly_damaging(0.767) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD |
PYCR2 | SNV | Missense_Mutation | c.624N>T | p.Gln208His | p.Q208H | Q96C36 | protein_coding | deleterious(0.04) | benign(0.399) | TCGA-BR-8591-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
PYCR2 | SNV | Missense_Mutation | novel | c.315G>C | p.Glu105Asp | p.E105D | Q96C36 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-D7-A74A-01 | Stomach | stomach adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
PYCR2 | SNV | Missense_Mutation | rs199945116 | c.598C>T | p.Arg200Cys | p.R200C | Q96C36 | protein_coding | deleterious(0.03) | possibly_damaging(0.86) | TCGA-FP-A4BE-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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