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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 |
| Page: 1 2 3 4 5 6 7 8 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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: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 |
| Page: 1 2 3 4 5 |
| 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 |
| 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 |
| PRDM2 | SNV | Missense_Mutation | c.1294N>A | p.Asp432Asn | p.D432N | Q13029 | protein_coding | tolerated(0.12) | benign(0) | TCGA-A2-A0EQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| PRDM2 | SNV | Missense_Mutation | c.3889N>T | p.Ser1297Cys | p.S1297C | Q13029 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PRDM2 | SNV | Missense_Mutation | c.4396N>C | p.Tyr1466His | p.Y1466H | Q13029 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PRDM2 | SNV | Missense_Mutation | c.1567G>C | p.Glu523Gln | p.E523Q | Q13029 | protein_coding | tolerated(0.3) | possibly_damaging(0.857) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PRDM2 | SNV | Missense_Mutation | rs200363632 | c.2299N>A | p.Gly767Arg | p.G767R | Q13029 | protein_coding | tolerated(0.53) | benign(0.013) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
| PRDM2 | SNV | Missense_Mutation | c.994N>C | p.Glu332Gln | p.E332Q | Q13029 | protein_coding | tolerated(0.06) | possibly_damaging(0.715) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD | |
| PRDM2 | SNV | Missense_Mutation | c.4739G>A | p.Arg1580Lys | p.R1580K | Q13029 | protein_coding | tolerated(0.15) | benign(0.069) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PRDM2 | SNV | Missense_Mutation | novel | c.940N>A | p.Glu314Lys | p.E314K | Q13029 | protein_coding | tolerated_low_confidence(0.08) | possibly_damaging(0.901) | TCGA-PE-A5DD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | CR | |
| PRDM2 | insertion | Nonsense_Mutation | novel | c.5001_5002insACCTTTTCTTTCCATTAAA | p.Asp1668ThrfsTer6 | p.D1668Tfs*6 | Q13029 | protein_coding | TCGA-A8-A07W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD | ||
| PRDM2 | insertion | Frame_Shift_Ins | novel | c.5003_5004insTCTAACCAAA | p.Gly1669LeufsTer36 | p.G1669Lfs*36 | Q13029 | protein_coding | TCGA-A8-A07W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
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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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