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Gene: PFDN2 |
Gene summary for PFDN2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PFDN2 | Gene ID | 5202 |
| Gene name | prefoldin subunit 2 | |
| Gene Alias | PFD2 | |
| Cytomap | 1q23.3 | |
| Gene Type | protein-coding | GO ID | GO:0006457 | UniProtAcc | B1AQP2 |
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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 |
| 5202 | PFDN2 | GSM4909282 | Human | Breast | IDC | 5.26e-41 | 6.72e-01 | -0.0288 |
| 5202 | PFDN2 | GSM4909285 | Human | Breast | IDC | 1.43e-17 | 5.03e-01 | 0.21 |
| 5202 | PFDN2 | GSM4909287 | Human | Breast | IDC | 2.91e-12 | 4.45e-01 | 0.2057 |
| 5202 | PFDN2 | GSM4909288 | Human | Breast | IDC | 7.47e-03 | 1.97e-01 | 0.0988 |
| 5202 | PFDN2 | GSM4909290 | Human | Breast | IDC | 4.96e-03 | 3.20e-01 | 0.2096 |
| 5202 | PFDN2 | GSM4909294 | Human | Breast | IDC | 3.80e-04 | 1.43e-01 | 0.2022 |
| 5202 | PFDN2 | GSM4909296 | Human | Breast | IDC | 1.17e-10 | -5.49e-02 | 0.1524 |
| 5202 | PFDN2 | GSM4909297 | Human | Breast | IDC | 2.44e-19 | -2.62e-01 | 0.1517 |
| 5202 | PFDN2 | GSM4909308 | Human | Breast | IDC | 3.02e-03 | 2.56e-01 | 0.158 |
| 5202 | PFDN2 | GSM4909311 | Human | Breast | IDC | 9.86e-43 | -3.39e-01 | 0.1534 |
| 5202 | PFDN2 | GSM4909312 | Human | Breast | IDC | 3.72e-15 | -1.22e-01 | 0.1552 |
| 5202 | PFDN2 | GSM4909315 | Human | Breast | IDC | 3.48e-02 | 2.63e-01 | 0.21 |
| 5202 | PFDN2 | GSM4909316 | Human | Breast | IDC | 2.00e-04 | 2.62e-01 | 0.21 |
| 5202 | PFDN2 | GSM4909319 | Human | Breast | IDC | 4.22e-44 | -3.52e-01 | 0.1563 |
| 5202 | PFDN2 | GSM4909320 | Human | Breast | IDC | 2.21e-07 | -1.97e-01 | 0.1575 |
| 5202 | PFDN2 | GSM4909321 | Human | Breast | IDC | 2.01e-15 | -9.24e-02 | 0.1559 |
| 5202 | PFDN2 | brca1 | Human | Breast | Precancer | 1.73e-05 | 3.41e-01 | -0.0338 |
| 5202 | PFDN2 | M2 | Human | Breast | IDC | 3.94e-03 | 2.75e-01 | 0.21 |
| 5202 | PFDN2 | NCCBC14 | Human | Breast | DCIS | 2.74e-12 | 3.76e-02 | 0.2021 |
| 5202 | PFDN2 | NCCBC3 | Human | Breast | DCIS | 1.01e-04 | -1.64e-01 | 0.1198 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| 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 | ||
| 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:00064578 | Breast | Precancer | protein folding | 43/1080 | 212/18723 | 3.48e-13 | 7.45e-11 | 43 |
| GO:19029039 | Breast | Precancer | regulation of supramolecular fiber organization | 42/1080 | 383/18723 | 4.92e-05 | 1.04e-03 | 42 |
| GO:19900005 | Breast | Precancer | amyloid fibril formation | 9/1080 | 34/18723 | 9.66e-05 | 1.80e-03 | 9 |
| GO:00514959 | Breast | Precancer | positive regulation of cytoskeleton organization | 28/1080 | 226/18723 | 1.13e-04 | 2.04e-03 | 28 |
| GO:19059063 | Breast | Precancer | regulation of amyloid fibril formation | 5/1080 | 16/18723 | 1.62e-03 | 1.64e-02 | 5 |
| GO:19059073 | Breast | Precancer | negative regulation of amyloid fibril formation | 4/1080 | 13/18723 | 5.17e-03 | 3.86e-02 | 4 |
| GO:000645713 | Breast | IDC | protein folding | 47/1434 | 212/18723 | 2.31e-11 | 3.86e-09 | 47 |
| GO:199000012 | Breast | IDC | amyloid fibril formation | 12/1434 | 34/18723 | 4.35e-06 | 1.53e-04 | 12 |
| GO:190290314 | Breast | IDC | regulation of supramolecular fiber organization | 54/1434 | 383/18723 | 9.40e-06 | 2.66e-04 | 54 |
| GO:005149513 | Breast | IDC | positive regulation of cytoskeleton organization | 35/1434 | 226/18723 | 5.04e-05 | 1.09e-03 | 35 |
| GO:190590611 | Breast | IDC | regulation of amyloid fibril formation | 7/1434 | 16/18723 | 9.40e-05 | 1.81e-03 | 7 |
| GO:190590711 | Breast | IDC | negative regulation of amyloid fibril formation | 6/1434 | 13/18723 | 2.14e-04 | 3.45e-03 | 6 |
| GO:000645723 | Breast | DCIS | protein folding | 47/1390 | 212/18723 | 7.84e-12 | 1.53e-09 | 47 |
| GO:199000021 | Breast | DCIS | amyloid fibril formation | 12/1390 | 34/18723 | 3.15e-06 | 1.02e-04 | 12 |
| GO:190290324 | Breast | DCIS | regulation of supramolecular fiber organization | 54/1390 | 383/18723 | 3.82e-06 | 1.16e-04 | 54 |
| GO:005149523 | Breast | DCIS | positive regulation of cytoskeleton organization | 35/1390 | 226/18723 | 2.66e-05 | 6.04e-04 | 35 |
| GO:19059062 | Breast | DCIS | regulation of amyloid fibril formation | 7/1390 | 16/18723 | 7.70e-05 | 1.48e-03 | 7 |
| GO:19059072 | Breast | DCIS | negative regulation of amyloid fibril formation | 6/1390 | 13/18723 | 1.80e-04 | 2.96e-03 | 6 |
| GO:190290310 | Cervix | CC | regulation of supramolecular fiber organization | 92/2311 | 383/18723 | 1.49e-10 | 2.48e-08 | 92 |
| GO:19029048 | Cervix | CC | negative regulation of supramolecular fiber organization | 40/2311 | 167/18723 | 2.39e-05 | 4.17e-04 | 40 |
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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 |
| 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 |
| PFDN2 | SNV | Missense_Mutation | c.11N>G | p.Asn4Ser | p.N4S | Q9UHV9 | protein_coding | tolerated_low_confidence(0.23) | benign(0) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| PFDN2 | SNV | Missense_Mutation | c.125N>A | p.Ser42Tyr | p.S42Y | Q9UHV9 | protein_coding | deleterious(0) | probably_damaging(0.959) | TCGA-FU-A3HY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| PFDN2 | SNV | Missense_Mutation | novel | c.197A>C | p.Glu66Ala | p.E66A | Q9UHV9 | protein_coding | tolerated(0.23) | benign(0.003) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
| PFDN2 | SNV | Missense_Mutation | rs780121999 | c.374G>A | p.Arg125His | p.R125H | Q9UHV9 | protein_coding | tolerated(0.07) | probably_damaging(0.96) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PFDN2 | SNV | Missense_Mutation | novel | c.107N>G | p.Glu36Gly | p.E36G | Q9UHV9 | protein_coding | deleterious(0) | possibly_damaging(0.657) | TCGA-D1-A0ZP-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| PFDN2 | SNV | Missense_Mutation | novel | c.91N>G | p.Asn31Asp | p.N31D | Q9UHV9 | protein_coding | tolerated(0.06) | possibly_damaging(0.841) | TCGA-D1-A175-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
| PFDN2 | SNV | Missense_Mutation | c.349N>A | p.Glu117Lys | p.E117K | Q9UHV9 | protein_coding | tolerated(0.09) | benign(0.211) | TCGA-69-7979-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PFDN2 | SNV | Missense_Mutation | novel | c.385G>A | p.Glu129Lys | p.E129K | Q9UHV9 | protein_coding | tolerated(0.12) | probably_damaging(0.95) | TCGA-CR-6484-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Chemotherapy | carboplatin | SD |
| PFDN2 | SNV | Missense_Mutation | novel | c.275N>G | p.Asn92Ser | p.N92S | Q9UHV9 | protein_coding | tolerated(0.67) | benign(0.026) | TCGA-CV-7416-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| PFDN2 | SNV | Missense_Mutation | c.100N>T | p.Arg34Trp | p.R34W | Q9UHV9 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-BR-8361-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | 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 |
| Page: 1 |
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