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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 |
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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:000645727 | Thyroid | HT | protein folding | 45/1272 | 212/18723 | 5.29e-12 | 1.01e-09 | 45 |
GO:003497627 | Thyroid | HT | response to endoplasmic reticulum stress | 41/1272 | 256/18723 | 2.43e-07 | 1.20e-05 | 41 |
GO:009719129 | Thyroid | HT | extrinsic apoptotic signaling pathway | 36/1272 | 219/18723 | 6.85e-07 | 2.80e-05 | 36 |
GO:200123629 | Thyroid | HT | regulation of extrinsic apoptotic signaling pathway | 28/1272 | 151/18723 | 1.02e-06 | 4.03e-05 | 28 |
GO:003497526 | Thyroid | HT | protein folding in endoplasmic reticulum | 7/1272 | 11/18723 | 1.70e-06 | 6.40e-05 | 7 |
GO:009876024 | Thyroid | HT | response to interleukin-7 | 8/1272 | 15/18723 | 1.86e-06 | 6.84e-05 | 8 |
GO:009876124 | Thyroid | HT | cellular response to interleukin-7 | 8/1272 | 15/18723 | 1.86e-06 | 6.84e-05 | 8 |
GO:200123527 | Thyroid | HT | positive regulation of apoptotic signaling pathway | 23/1272 | 126/18723 | 1.20e-05 | 3.15e-04 | 23 |
GO:0034976113 | Thyroid | PTC | response to endoplasmic reticulum stress | 161/5968 | 256/18723 | 1.14e-24 | 3.27e-22 | 161 |
GO:0006457112 | Thyroid | PTC | protein folding | 137/5968 | 212/18723 | 8.29e-23 | 2.01e-20 | 137 |
GO:2001233113 | Thyroid | PTC | regulation of apoptotic signaling pathway | 197/5968 | 356/18723 | 2.58e-20 | 3.69e-18 | 197 |
GO:0097191113 | Thyroid | PTC | extrinsic apoptotic signaling pathway | 117/5968 | 219/18723 | 2.73e-11 | 1.03e-09 | 117 |
GO:2001236113 | Thyroid | PTC | regulation of extrinsic apoptotic signaling pathway | 82/5968 | 151/18723 | 9.01e-09 | 2.18e-07 | 82 |
GO:2001235112 | Thyroid | PTC | positive regulation of apoptotic signaling pathway | 69/5968 | 126/18723 | 8.51e-08 | 1.73e-06 | 69 |
GO:200123820 | Thyroid | PTC | positive regulation of extrinsic apoptotic signaling pathway | 30/5968 | 48/18723 | 1.23e-05 | 1.34e-04 | 30 |
GO:0034975110 | Thyroid | PTC | protein folding in endoplasmic reticulum | 10/5968 | 11/18723 | 8.42e-05 | 7.03e-04 | 10 |
GO:0098760111 | Thyroid | PTC | response to interleukin-7 | 10/5968 | 15/18723 | 5.94e-03 | 2.64e-02 | 10 |
GO:0098761111 | Thyroid | PTC | cellular response to interleukin-7 | 10/5968 | 15/18723 | 5.94e-03 | 2.64e-02 | 10 |
GO:003497633 | Thyroid | ATC | response to endoplasmic reticulum stress | 167/6293 | 256/18723 | 2.62e-25 | 1.03e-22 | 167 |
GO:000645733 | Thyroid | ATC | protein folding | 140/6293 | 212/18723 | 3.46e-22 | 8.09e-20 | 140 |
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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 |
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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 |
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 |
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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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