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Gene: PRDX2 |
Gene summary for PRDX2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PRDX2 | Gene ID | 7001 |
Gene name | peroxiredoxin 2 | |
Gene Alias | HEL-S-2a | |
Cytomap | 19p13.13 | |
Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | P32119 |
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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 |
7001 | PRDX2 | GSM4909281 | Human | Breast | IDC | 1.18e-02 | 3.08e-01 | 0.21 |
7001 | PRDX2 | GSM4909282 | Human | Breast | IDC | 6.87e-39 | 6.09e-01 | -0.0288 |
7001 | PRDX2 | GSM4909285 | Human | Breast | IDC | 4.48e-60 | 8.36e-01 | 0.21 |
7001 | PRDX2 | GSM4909286 | Human | Breast | IDC | 6.82e-03 | 1.06e-01 | 0.1081 |
7001 | PRDX2 | GSM4909287 | Human | Breast | IDC | 4.67e-12 | 3.41e-01 | 0.2057 |
7001 | PRDX2 | GSM4909289 | Human | Breast | IDC | 7.11e-06 | 4.58e-01 | 0.1064 |
7001 | PRDX2 | GSM4909290 | Human | Breast | IDC | 2.92e-18 | 5.08e-01 | 0.2096 |
7001 | PRDX2 | GSM4909291 | Human | Breast | IDC | 1.69e-03 | 2.53e-01 | 0.1753 |
7001 | PRDX2 | GSM4909293 | Human | Breast | IDC | 5.60e-14 | 4.91e-01 | 0.1581 |
7001 | PRDX2 | GSM4909294 | Human | Breast | IDC | 7.78e-26 | 4.87e-01 | 0.2022 |
7001 | PRDX2 | GSM4909296 | Human | Breast | IDC | 1.93e-27 | 3.68e-01 | 0.1524 |
7001 | PRDX2 | GSM4909297 | Human | Breast | IDC | 2.46e-22 | 1.06e-01 | 0.1517 |
7001 | PRDX2 | GSM4909301 | Human | Breast | IDC | 2.42e-04 | 2.52e-01 | 0.1577 |
7001 | PRDX2 | GSM4909302 | Human | Breast | IDC | 2.82e-07 | 2.14e-01 | 0.1545 |
7001 | PRDX2 | GSM4909304 | Human | Breast | IDC | 6.66e-42 | 7.09e-01 | 0.1636 |
7001 | PRDX2 | GSM4909305 | Human | Breast | IDC | 1.98e-02 | 1.96e-01 | 0.0436 |
7001 | PRDX2 | GSM4909306 | Human | Breast | IDC | 1.79e-20 | 5.49e-01 | 0.1564 |
7001 | PRDX2 | GSM4909307 | Human | Breast | IDC | 1.45e-15 | 4.35e-01 | 0.1569 |
7001 | PRDX2 | GSM4909308 | Human | Breast | IDC | 2.01e-34 | 6.23e-01 | 0.158 |
7001 | PRDX2 | GSM4909309 | Human | Breast | IDC | 4.81e-02 | 9.66e-02 | 0.0483 |
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Transcriptomic changes along malignancy continuum. |
∗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 | CRC | |
Stomach | GC | |
Stomach | CAG with IM | |
Stomach | CSG | |
Stomach | CAG |
∗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:20012339 | Breast | Precancer | regulation of apoptotic signaling pathway | 65/1080 | 356/18723 | 7.70e-17 | 3.17e-14 | 65 |
GO:00069799 | Breast | Precancer | response to oxidative stress | 70/1080 | 446/18723 | 1.59e-14 | 4.26e-12 | 70 |
GO:00621979 | Breast | Precancer | cellular response to chemical stress | 51/1080 | 337/18723 | 2.40e-10 | 2.34e-08 | 51 |
GO:20012349 | Breast | Precancer | negative regulation of apoptotic signaling pathway | 39/1080 | 224/18723 | 5.35e-10 | 4.77e-08 | 39 |
GO:00003029 | Breast | Precancer | response to reactive oxygen species | 38/1080 | 222/18723 | 1.47e-09 | 1.23e-07 | 38 |
GO:00345999 | Breast | Precancer | cellular response to oxidative stress | 42/1080 | 288/18723 | 2.78e-08 | 1.79e-06 | 42 |
GO:00988698 | Breast | Precancer | cellular oxidant detoxification | 20/1080 | 101/18723 | 1.07e-06 | 4.18e-05 | 20 |
GO:00454548 | Breast | Precancer | cell redox homeostasis | 11/1080 | 35/18723 | 2.59e-06 | 8.65e-05 | 11 |
GO:19907488 | Breast | Precancer | cellular detoxification | 21/1080 | 116/18723 | 2.67e-06 | 8.89e-05 | 21 |
GO:00420609 | Breast | Precancer | wound healing | 48/1080 | 422/18723 | 5.48e-06 | 1.63e-04 | 48 |
GO:20012369 | Breast | Precancer | regulation of extrinsic apoptotic signaling pathway | 24/1080 | 151/18723 | 5.78e-06 | 1.70e-04 | 24 |
GO:00022378 | Breast | Precancer | response to molecule of bacterial origin | 43/1080 | 363/18723 | 6.05e-06 | 1.72e-04 | 43 |
GO:00487329 | Breast | Precancer | gland development | 49/1080 | 436/18723 | 6.11e-06 | 1.73e-04 | 49 |
GO:00987548 | Breast | Precancer | detoxification | 24/1080 | 152/18723 | 6.49e-06 | 1.81e-04 | 24 |
GO:00324968 | Breast | Precancer | response to lipopolysaccharide | 41/1080 | 343/18723 | 7.94e-06 | 2.17e-04 | 41 |
GO:00972378 | Breast | Precancer | cellular response to toxic substance | 21/1080 | 124/18723 | 7.98e-06 | 2.17e-04 | 21 |
GO:00971919 | Breast | Precancer | extrinsic apoptotic signaling pathway | 30/1080 | 219/18723 | 9.42e-06 | 2.50e-04 | 30 |
GO:00421107 | Breast | Precancer | T cell activation | 52/1080 | 487/18723 | 1.37e-05 | 3.42e-04 | 52 |
GO:00346149 | Breast | Precancer | cellular response to reactive oxygen species | 23/1080 | 155/18723 | 2.82e-05 | 6.31e-04 | 23 |
GO:19037069 | Breast | Precancer | regulation of hemopoiesis | 41/1080 | 367/18723 | 3.95e-05 | 8.52e-04 | 41 |
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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 |
PRDX2 | SNV | Missense_Mutation | novel | c.544A>T | p.Thr182Ser | p.T182S | P32119 | protein_coding | deleterious(0.03) | possibly_damaging(0.515) | TCGA-A7-A4SA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
PRDX2 | SNV | Missense_Mutation | novel | c.565N>T | p.Asp189Tyr | p.D189Y | P32119 | protein_coding | deleterious(0.01) | benign(0.102) | TCGA-OL-A66L-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PRDX2 | insertion | Frame_Shift_Ins | novel | c.245_246insGGGAGGAGGTTGCAGTAAG | p.His83GlyfsTer30 | p.H83Gfs*30 | P32119 | protein_coding | TCGA-A2-A0EV-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | ||
PRDX2 | SNV | Missense_Mutation | novel | c.169N>A | p.Ala57Thr | p.A57T | P32119 | protein_coding | deleterious(0.01) | probably_damaging(0.97) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PRDX2 | SNV | Missense_Mutation | novel | c.452C>T | p.Ser151Phe | p.S151F | P32119 | protein_coding | deleterious(0.03) | probably_damaging(0.996) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PRDX2 | SNV | Missense_Mutation | rs534702204 | c.334T>C | p.Ser112Pro | p.S112P | P32119 | protein_coding | deleterious(0) | probably_damaging(0.975) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
PRDX2 | SNV | Missense_Mutation | rs755166073 | c.448N>T | p.Arg150Cys | p.R150C | P32119 | protein_coding | deleterious(0.05) | probably_damaging(0.98) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
PRDX2 | SNV | Missense_Mutation | rs764907738 | c.559N>A | p.Val187Met | p.V187M | P32119 | protein_coding | tolerated(0.06) | benign(0.376) | TCGA-CM-4746-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
PRDX2 | SNV | Missense_Mutation | rs369634820 | c.272G>A | p.Arg91Gln | p.R91Q | P32119 | protein_coding | deleterious(0.03) | possibly_damaging(0.74) | TCGA-D5-7000-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PRDX2 | SNV | Missense_Mutation | c.38N>T | p.Pro13Leu | p.P13L | P32119 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | 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 |
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