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Gene: PRDM2 |
Gene summary for PRDM2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PRDM2 | Gene ID | 7799 |
Gene name | PR/SET domain 2 | |
Gene Alias | HUMHOXY1 | |
Cytomap | 1p36.21 | |
Gene Type | protein-coding | GO ID | GO:0000122 | UniProtAcc | Q13029 |
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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 |
7799 | PRDM2 | CCI_1 | Human | Cervix | CC | 8.25e-03 | 5.77e-01 | 0.528 |
7799 | PRDM2 | CCI_2 | Human | Cervix | CC | 5.10e-06 | 1.06e+00 | 0.5249 |
7799 | PRDM2 | CCI_3 | Human | Cervix | CC | 8.69e-03 | 5.74e-01 | 0.516 |
7799 | PRDM2 | AEH-subject1 | Human | Endometrium | AEH | 4.27e-13 | 4.36e-01 | -0.3059 |
7799 | PRDM2 | AEH-subject2 | Human | Endometrium | AEH | 1.47e-05 | 2.32e-01 | -0.2525 |
7799 | PRDM2 | AEH-subject3 | Human | Endometrium | AEH | 4.25e-02 | 1.92e-01 | -0.2576 |
7799 | PRDM2 | AEH-subject4 | Human | Endometrium | AEH | 7.43e-13 | 4.79e-01 | -0.2657 |
7799 | PRDM2 | AEH-subject5 | Human | Endometrium | AEH | 6.96e-09 | 4.76e-01 | -0.2953 |
7799 | PRDM2 | EEC-subject1 | Human | Endometrium | EEC | 1.42e-13 | 5.15e-01 | -0.2682 |
7799 | PRDM2 | EEC-subject3 | Human | Endometrium | EEC | 1.91e-05 | 1.23e-01 | -0.2525 |
7799 | PRDM2 | EEC-subject4 | Human | Endometrium | EEC | 5.32e-03 | 2.73e-01 | -0.2571 |
7799 | PRDM2 | EEC-subject5 | Human | Endometrium | EEC | 3.93e-05 | 3.53e-01 | -0.249 |
7799 | PRDM2 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 3.22e-09 | -1.51e-01 | -0.1869 |
7799 | PRDM2 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 1.96e-09 | -1.45e-01 | -0.1875 |
7799 | PRDM2 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 5.33e-08 | -7.34e-02 | -0.1883 |
7799 | PRDM2 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 4.29e-10 | -9.49e-02 | -0.1934 |
7799 | PRDM2 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 1.61e-21 | -9.42e-02 | -0.1917 |
7799 | PRDM2 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 2.73e-15 | -8.68e-02 | -0.1916 |
7799 | PRDM2 | LZE4T | Human | Esophagus | ESCC | 4.59e-03 | 4.89e-02 | 0.0811 |
7799 | PRDM2 | LZE7T | Human | Esophagus | ESCC | 8.79e-12 | 4.28e-01 | 0.0667 |
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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 | 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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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00075689 | Cervix | CC | aging | 75/2311 | 339/18723 | 2.75e-07 | 1.13e-05 | 75 |
GO:00165705 | Cervix | CC | histone modification | 84/2311 | 463/18723 | 1.70e-04 | 2.01e-03 | 84 |
GO:00165715 | Cervix | CC | histone methylation | 30/2311 | 141/18723 | 1.88e-03 | 1.39e-02 | 30 |
GO:00064795 | Cervix | CC | protein methylation | 36/2311 | 181/18723 | 2.46e-03 | 1.71e-02 | 36 |
GO:00082135 | Cervix | CC | protein alkylation | 36/2311 | 181/18723 | 2.46e-03 | 1.71e-02 | 36 |
GO:000756810 | Endometrium | AEH | aging | 59/2100 | 339/18723 | 4.00e-04 | 4.28e-03 | 59 |
GO:000756815 | Endometrium | EEC | aging | 66/2168 | 339/18723 | 1.46e-05 | 2.87e-04 | 66 |
GO:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
GO:00434143 | Esophagus | ESCC | macromolecule methylation | 199/8552 | 316/18723 | 3.44e-10 | 9.57e-09 | 199 |
GO:00322592 | Esophagus | ESCC | methylation | 222/8552 | 364/18723 | 2.26e-09 | 5.09e-08 | 222 |
GO:000756820 | Esophagus | ESCC | aging | 201/8552 | 339/18723 | 2.64e-07 | 3.94e-06 | 201 |
GO:000647914 | Esophagus | ESCC | protein methylation | 115/8552 | 181/18723 | 9.07e-07 | 1.16e-05 | 115 |
GO:000821314 | Esophagus | ESCC | protein alkylation | 115/8552 | 181/18723 | 9.07e-07 | 1.16e-05 | 115 |
GO:00165718 | Esophagus | ESCC | histone methylation | 89/8552 | 141/18723 | 2.17e-05 | 1.87e-04 | 89 |
GO:00165703 | Liver | NAFLD | histone modification | 90/1882 | 463/18723 | 5.74e-10 | 1.28e-07 | 90 |
GO:00165713 | Liver | NAFLD | histone methylation | 29/1882 | 141/18723 | 1.40e-04 | 2.63e-03 | 29 |
GO:00064793 | Liver | NAFLD | protein methylation | 33/1882 | 181/18723 | 5.36e-04 | 7.35e-03 | 33 |
GO:00082133 | Liver | NAFLD | protein alkylation | 33/1882 | 181/18723 | 5.36e-04 | 7.35e-03 | 33 |
GO:00075687 | Liver | NAFLD | aging | 53/1882 | 339/18723 | 7.78e-04 | 9.77e-03 | 53 |
GO:0043414 | Liver | NAFLD | macromolecule methylation | 47/1882 | 316/18723 | 4.08e-03 | 3.41e-02 | 47 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0031010 | Esophagus | ESCC | Lysine degradation | 41/4205 | 63/8465 | 9.63e-03 | 2.27e-02 | 1.16e-02 | 41 |
hsa0031013 | Esophagus | ESCC | Lysine degradation | 41/4205 | 63/8465 | 9.63e-03 | 2.27e-02 | 1.16e-02 | 41 |
hsa003108 | Liver | NAFLD | Lysine degradation | 21/1043 | 63/8465 | 1.09e-05 | 3.58e-04 | 2.89e-04 | 21 |
hsa0031011 | Liver | NAFLD | Lysine degradation | 21/1043 | 63/8465 | 1.09e-05 | 3.58e-04 | 2.89e-04 | 21 |
hsa0031041 | Liver | HCC | Lysine degradation | 47/4020 | 63/8465 | 1.02e-05 | 7.58e-05 | 4.22e-05 | 47 |
hsa0031051 | Liver | HCC | Lysine degradation | 47/4020 | 63/8465 | 1.02e-05 | 7.58e-05 | 4.22e-05 | 47 |
hsa003109 | Lung | IAC | Lysine degradation | 17/1053 | 63/8465 | 1.35e-03 | 8.63e-03 | 5.73e-03 | 17 |
hsa0031012 | Lung | IAC | Lysine degradation | 17/1053 | 63/8465 | 1.35e-03 | 8.63e-03 | 5.73e-03 | 17 |
hsa0031022 | Lung | AIS | Lysine degradation | 16/961 | 63/8465 | 1.41e-03 | 9.49e-03 | 6.07e-03 | 16 |
hsa0031032 | Lung | AIS | Lysine degradation | 16/961 | 63/8465 | 1.41e-03 | 9.49e-03 | 6.07e-03 | 16 |
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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 |
PRDM2 | SNV | Missense_Mutation | c.1514N>C | p.Val505Ala | p.V505A | Q13029 | protein_coding | deleterious(0) | probably_damaging(0.954) | TCGA-BR-8487-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
PRDM2 | SNV | Missense_Mutation | c.1600N>G | p.Thr534Ala | p.T534A | Q13029 | protein_coding | tolerated(1) | benign(0.018) | TCGA-BR-8487-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
PRDM2 | SNV | Missense_Mutation | c.2411N>C | p.Lys804Thr | p.K804T | Q13029 | protein_coding | tolerated(0.18) | possibly_damaging(0.838) | TCGA-BR-8680-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | CR | |
PRDM2 | SNV | Missense_Mutation | c.4631N>C | p.Val1544Ala | p.V1544A | Q13029 | protein_coding | tolerated(1) | benign(0) | TCGA-BR-8680-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | oxaliplatin | CR | |
PRDM2 | SNV | Missense_Mutation | rs201537864 | c.470C>T | p.Ala157Val | p.A157V | Q13029 | protein_coding | deleterious(0.03) | benign(0.012) | TCGA-BR-A4QL-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | xeloda | CR |
PRDM2 | SNV | Missense_Mutation | c.1217G>A | p.Arg406Gln | p.R406Q | Q13029 | protein_coding | deleterious(0.01) | probably_damaging(0.986) | TCGA-CG-5723-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
PRDM2 | SNV | Missense_Mutation | rs138768059 | c.3046G>A | p.Ala1016Thr | p.A1016T | Q13029 | protein_coding | tolerated(1) | benign(0.003) | TCGA-CG-5723-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
PRDM2 | SNV | Missense_Mutation | rs148030242 | c.1564N>C | p.Glu522Gln | p.E522Q | Q13029 | protein_coding | tolerated(0.22) | benign(0.093) | TCGA-D7-5578-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
PRDM2 | SNV | Missense_Mutation | c.4235T>C | p.Met1412Thr | p.M1412T | Q13029 | protein_coding | tolerated(0.15) | benign(0.003) | TCGA-FP-A4BE-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
PRDM2 | SNV | Missense_Mutation | rs556843220 | c.834N>T | p.Glu278Asp | p.E278D | Q13029 | protein_coding | tolerated(0.64) | benign(0) | TCGA-HF-A5NB-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | fluorouracil | 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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