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Gene: PDIA3 |
Gene summary for PDIA3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PDIA3 | Gene ID | 2923 |
| Gene name | protein disulfide isomerase family A member 3 | |
| Gene Alias | ER60 | |
| Cytomap | 15q15.3 | |
| Gene Type | protein-coding | GO ID | GO:0006457 | UniProtAcc | P30101 |
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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 |
| 2923 | PDIA3 | CA_HPV_1 | Human | Cervix | CC | 5.34e-05 | -9.93e-02 | 0.0264 |
| 2923 | PDIA3 | CA_HPV_3 | Human | Cervix | CC | 2.40e-08 | -6.15e-02 | 0.0414 |
| 2923 | PDIA3 | HSIL_HPV_2 | Human | Cervix | HSIL_HPV | 4.91e-02 | -1.85e-01 | 0.0208 |
| 2923 | PDIA3 | N_HPV_2 | Human | Cervix | N_HPV | 8.38e-05 | -1.30e-02 | -0.0131 |
| 2923 | PDIA3 | CCI_3 | Human | Cervix | CC | 1.47e-03 | -5.09e-01 | 0.516 |
| 2923 | PDIA3 | CCII_1 | Human | Cervix | CC | 1.09e-27 | -9.56e-01 | 0.3249 |
| 2923 | PDIA3 | sample3 | Human | Cervix | CC | 3.87e-08 | 1.82e-01 | 0.1387 |
| 2923 | PDIA3 | L1 | Human | Cervix | CC | 5.30e-09 | -4.66e-01 | 0.0802 |
| 2923 | PDIA3 | T3 | Human | Cervix | CC | 6.99e-07 | 1.97e-01 | 0.1389 |
| 2923 | PDIA3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.39e-03 | 2.02e-01 | 0.0155 |
| 2923 | PDIA3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.05e-05 | 6.21e-01 | -0.1808 |
| 2923 | PDIA3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 3.36e-27 | 1.05e+00 | -0.0811 |
| 2923 | PDIA3 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.09e-26 | 1.10e+00 | -0.1088 |
| 2923 | PDIA3 | HTA11_347_2000001011 | Human | Colorectum | AD | 3.79e-43 | 1.08e+00 | -0.1954 |
| 2923 | PDIA3 | HTA11_411_2000001011 | Human | Colorectum | SER | 2.60e-10 | 1.13e+00 | -0.2602 |
| 2923 | PDIA3 | HTA11_2112_2000001011 | Human | Colorectum | SER | 5.38e-07 | 1.06e+00 | -0.2196 |
| 2923 | PDIA3 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.67e-22 | 1.07e+00 | -0.1526 |
| 2923 | PDIA3 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.40e-16 | 7.55e-01 | -0.1464 |
| 2923 | PDIA3 | HTA11_866_2000001011 | Human | Colorectum | AD | 2.02e-02 | 3.56e-01 | -0.1001 |
| 2923 | PDIA3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 5.08e-29 | 1.38e+00 | -0.059 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| 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 | ||
| 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 | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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:200123310 | Cervix | CC | regulation of apoptotic signaling pathway | 96/2311 | 356/18723 | 4.08e-14 | 3.05e-11 | 96 |
| GO:20012357 | Cervix | CC | positive regulation of apoptotic signaling pathway | 37/2311 | 126/18723 | 2.70e-07 | 1.12e-05 | 37 |
| GO:009719110 | Cervix | CC | extrinsic apoptotic signaling pathway | 52/2311 | 219/18723 | 2.06e-06 | 6.34e-05 | 52 |
| GO:003497610 | Cervix | CC | response to endoplasmic reticulum stress | 57/2311 | 256/18723 | 5.81e-06 | 1.42e-04 | 57 |
| GO:200123610 | Cervix | CC | regulation of extrinsic apoptotic signaling pathway | 37/2311 | 151/18723 | 2.80e-05 | 4.65e-04 | 37 |
| GO:00349759 | Cervix | CC | protein folding in endoplasmic reticulum | 7/2311 | 11/18723 | 9.07e-05 | 1.20e-03 | 7 |
| GO:00064579 | Cervix | CC | protein folding | 44/2311 | 212/18723 | 3.43e-04 | 3.59e-03 | 44 |
| GO:00987609 | Cervix | CC | response to interleukin-7 | 7/2311 | 15/18723 | 1.13e-03 | 9.29e-03 | 7 |
| GO:00987619 | Cervix | CC | cellular response to interleukin-7 | 7/2311 | 15/18723 | 1.13e-03 | 9.29e-03 | 7 |
| GO:20012386 | Cervix | CC | positive regulation of extrinsic apoptotic signaling pathway | 14/2311 | 48/18723 | 1.48e-03 | 1.15e-02 | 14 |
| GO:200123315 | Cervix | HSIL_HPV | regulation of apoptotic signaling pathway | 46/737 | 356/18723 | 1.23e-12 | 1.49e-09 | 46 |
| GO:200123515 | Cervix | HSIL_HPV | positive regulation of apoptotic signaling pathway | 21/737 | 126/18723 | 2.07e-08 | 1.95e-06 | 21 |
| GO:000645714 | Cervix | HSIL_HPV | protein folding | 20/737 | 212/18723 | 2.81e-04 | 4.69e-03 | 20 |
| GO:200123615 | Cervix | HSIL_HPV | regulation of extrinsic apoptotic signaling pathway | 16/737 | 151/18723 | 3.08e-04 | 5.01e-03 | 16 |
| GO:009719115 | Cervix | HSIL_HPV | extrinsic apoptotic signaling pathway | 20/737 | 219/18723 | 4.29e-04 | 6.42e-03 | 20 |
| GO:003497514 | Cervix | HSIL_HPV | protein folding in endoplasmic reticulum | 4/737 | 11/18723 | 6.30e-04 | 8.64e-03 | 4 |
| GO:200123813 | Cervix | HSIL_HPV | positive regulation of extrinsic apoptotic signaling pathway | 7/737 | 48/18723 | 2.57e-03 | 2.50e-02 | 7 |
| GO:003497615 | Cervix | HSIL_HPV | response to endoplasmic reticulum stress | 20/737 | 256/18723 | 2.88e-03 | 2.70e-02 | 20 |
| GO:200123325 | Cervix | N_HPV | regulation of apoptotic signaling pathway | 36/534 | 356/18723 | 4.95e-11 | 5.63e-08 | 36 |
| GO:000645724 | Cervix | N_HPV | protein folding | 22/534 | 212/18723 | 1.90e-07 | 1.57e-05 | 22 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0461220 | Cervix | CC | Antigen processing and presentation | 34/1267 | 78/8465 | 1.06e-09 | 2.14e-08 | 1.26e-08 | 34 |
| hsa0414120 | Cervix | CC | Protein processing in endoplasmic reticulum | 55/1267 | 174/8465 | 1.74e-08 | 2.68e-07 | 1.58e-07 | 55 |
| hsa0516318 | Cervix | CC | Human cytomegalovirus infection | 65/1267 | 225/8465 | 4.59e-08 | 6.47e-07 | 3.83e-07 | 65 |
| hsa0516920 | Cervix | CC | Epstein-Barr virus infection | 57/1267 | 202/8465 | 7.30e-07 | 7.39e-06 | 4.37e-06 | 57 |
| hsa0517016 | Cervix | CC | Human immunodeficiency virus 1 infection | 55/1267 | 212/8465 | 1.80e-05 | 1.42e-04 | 8.40e-05 | 55 |
| hsa04612110 | Cervix | CC | Antigen processing and presentation | 34/1267 | 78/8465 | 1.06e-09 | 2.14e-08 | 1.26e-08 | 34 |
| hsa04141110 | Cervix | CC | Protein processing in endoplasmic reticulum | 55/1267 | 174/8465 | 1.74e-08 | 2.68e-07 | 1.58e-07 | 55 |
| hsa0516319 | Cervix | CC | Human cytomegalovirus infection | 65/1267 | 225/8465 | 4.59e-08 | 6.47e-07 | 3.83e-07 | 65 |
| hsa05169110 | Cervix | CC | Epstein-Barr virus infection | 57/1267 | 202/8465 | 7.30e-07 | 7.39e-06 | 4.37e-06 | 57 |
| hsa0517017 | Cervix | CC | Human immunodeficiency virus 1 infection | 55/1267 | 212/8465 | 1.80e-05 | 1.42e-04 | 8.40e-05 | 55 |
| hsa0461224 | Cervix | HSIL_HPV | Antigen processing and presentation | 21/459 | 78/8465 | 5.10e-10 | 3.74e-08 | 3.02e-08 | 21 |
| hsa0414125 | Cervix | HSIL_HPV | Protein processing in endoplasmic reticulum | 21/459 | 174/8465 | 4.54e-04 | 3.80e-03 | 3.07e-03 | 21 |
| hsa0516923 | Cervix | HSIL_HPV | Epstein-Barr virus infection | 22/459 | 202/8465 | 1.35e-03 | 9.68e-03 | 7.82e-03 | 22 |
| hsa0461234 | Cervix | HSIL_HPV | Antigen processing and presentation | 21/459 | 78/8465 | 5.10e-10 | 3.74e-08 | 3.02e-08 | 21 |
| hsa0414135 | Cervix | HSIL_HPV | Protein processing in endoplasmic reticulum | 21/459 | 174/8465 | 4.54e-04 | 3.80e-03 | 3.07e-03 | 21 |
| hsa0516933 | Cervix | HSIL_HPV | Epstein-Barr virus infection | 22/459 | 202/8465 | 1.35e-03 | 9.68e-03 | 7.82e-03 | 22 |
| hsa0461243 | Cervix | N_HPV | Antigen processing and presentation | 20/349 | 78/8465 | 2.61e-11 | 1.42e-09 | 1.11e-09 | 20 |
| hsa0414144 | Cervix | N_HPV | Protein processing in endoplasmic reticulum | 21/349 | 174/8465 | 8.84e-06 | 1.09e-04 | 8.55e-05 | 21 |
| hsa0516942 | Cervix | N_HPV | Epstein-Barr virus infection | 19/349 | 202/8465 | 6.54e-04 | 4.94e-03 | 3.86e-03 | 19 |
| hsa0461253 | Cervix | N_HPV | Antigen processing and presentation | 20/349 | 78/8465 | 2.61e-11 | 1.42e-09 | 1.11e-09 | 20 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 |
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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 |
| PDIA3 | SNV | Missense_Mutation | rs756782649 | c.830N>G | p.Asn277Ser | p.N277S | P30101 | protein_coding | deleterious(0.03) | benign(0.268) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PDIA3 | SNV | Missense_Mutation | c.46N>G | p.Leu16Val | p.L16V | P30101 | protein_coding | tolerated(0.33) | benign(0.209) | TCGA-IR-A3LK-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD | |
| PDIA3 | SNV | Missense_Mutation | c.1024N>C | p.Phe342Leu | p.F342L | P30101 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A6-6653-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| PDIA3 | SNV | Missense_Mutation | c.583N>A | p.Glu195Lys | p.E195K | P30101 | protein_coding | tolerated(1) | benign(0.001) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| PDIA3 | SNV | Missense_Mutation | novel | c.713N>G | p.Glu238Gly | p.E238G | P30101 | protein_coding | tolerated(0.05) | benign(0.074) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PDIA3 | SNV | Missense_Mutation | novel | c.1466N>C | p.Val489Ala | p.V489A | P30101 | protein_coding | tolerated(0.14) | benign(0.027) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| PDIA3 | SNV | Missense_Mutation | novel | c.756N>C | p.Lys252Asn | p.K252N | P30101 | protein_coding | tolerated(0.24) | possibly_damaging(0.838) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PDIA3 | SNV | Missense_Mutation | rs138119635 | c.911N>A | p.Arg304His | p.R304H | P30101 | protein_coding | tolerated(0.1) | probably_damaging(0.944) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PDIA3 | SNV | Missense_Mutation | rs757380536 | c.1030N>T | p.Arg344Cys | p.R344C | P30101 | protein_coding | tolerated(0.1) | probably_damaging(0.937) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
| PDIA3 | SNV | Missense_Mutation | novel | c.160N>A | p.Ala54Thr | p.A54T | P30101 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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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