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Gene: PCNA |
Gene summary for PCNA |
Gene summary. |
Gene information | Species | Human | Gene symbol | PCNA | Gene ID | 5111 |
Gene name | proliferating cell nuclear antigen | |
Gene Alias | ATLD2 | |
Cytomap | 20p12.3 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P12004 |
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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 |
5111 | PCNA | GSM4909281 | Human | Breast | IDC | 1.92e-06 | 2.96e-01 | 0.21 |
5111 | PCNA | GSM4909282 | Human | Breast | IDC | 1.54e-24 | 5.82e-01 | -0.0288 |
5111 | PCNA | GSM4909285 | Human | Breast | IDC | 9.22e-23 | 5.19e-01 | 0.21 |
5111 | PCNA | GSM4909288 | Human | Breast | IDC | 1.92e-03 | 3.95e-01 | 0.0988 |
5111 | PCNA | GSM4909298 | Human | Breast | IDC | 5.22e-04 | 2.09e-01 | 0.1551 |
5111 | PCNA | GSM4909311 | Human | Breast | IDC | 6.26e-03 | -1.10e-01 | 0.1534 |
5111 | PCNA | GSM4909319 | Human | Breast | IDC | 2.74e-07 | -4.81e-02 | 0.1563 |
5111 | PCNA | brca2 | Human | Breast | Precancer | 4.18e-06 | 2.44e-01 | -0.024 |
5111 | PCNA | M2 | Human | Breast | IDC | 1.98e-09 | 6.53e-01 | 0.21 |
5111 | PCNA | NCCBC14 | Human | Breast | DCIS | 1.86e-03 | 1.63e-01 | 0.2021 |
5111 | PCNA | NCCBC5 | Human | Breast | DCIS | 4.22e-07 | 3.47e-01 | 0.2046 |
5111 | PCNA | P1 | Human | Breast | IDC | 1.40e-05 | 6.24e-03 | 0.1527 |
5111 | PCNA | P2 | Human | Breast | IDC | 1.56e-02 | 3.51e-01 | 0.21 |
5111 | PCNA | DCIS2 | Human | Breast | DCIS | 8.61e-24 | 2.79e-02 | 0.0085 |
5111 | PCNA | CA_HPV_3 | Human | Cervix | CC | 1.87e-04 | 2.66e-01 | 0.0414 |
5111 | PCNA | Tumor | Human | Cervix | CC | 1.91e-14 | 5.58e-01 | 0.1241 |
5111 | PCNA | sample3 | Human | Cervix | CC | 2.99e-20 | 5.95e-01 | 0.1387 |
5111 | PCNA | T3 | Human | Cervix | CC | 2.42e-25 | 6.42e-01 | 0.1389 |
5111 | PCNA | HTA11_1938_2000001011 | Human | Colorectum | AD | 5.14e-08 | 3.94e-01 | -0.0811 |
5111 | PCNA | HTA11_78_2000001011 | Human | Colorectum | AD | 2.49e-06 | 3.68e-01 | -0.1088 |
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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:00345991 | Colorectum | SER | cellular response to oxidative stress | 73/2897 | 288/18723 | 8.52e-06 | 2.86e-04 | 73 |
GO:00425421 | Colorectum | SER | response to hydrogen peroxide | 42/2897 | 146/18723 | 3.10e-05 | 8.27e-04 | 42 |
GO:20002781 | Colorectum | SER | regulation of DNA biosynthetic process | 33/2897 | 106/18723 | 3.83e-05 | 9.82e-04 | 33 |
GO:00510541 | Colorectum | SER | positive regulation of DNA metabolic process | 53/2897 | 201/18723 | 4.51e-05 | 1.13e-03 | 53 |
GO:00485451 | Colorectum | SER | response to steroid hormone | 80/2897 | 339/18723 | 5.15e-05 | 1.25e-03 | 80 |
GO:00510521 | Colorectum | SER | regulation of DNA metabolic process | 83/2897 | 359/18723 | 8.03e-05 | 1.77e-03 | 83 |
GO:00320691 | Colorectum | SER | regulation of nuclease activity | 11/2897 | 22/18723 | 1.60e-04 | 3.08e-03 | 11 |
GO:00100381 | Colorectum | SER | response to metal ion | 84/2897 | 373/18723 | 1.87e-04 | 3.44e-03 | 84 |
GO:20005731 | Colorectum | SER | positive regulation of DNA biosynthetic process | 22/2897 | 66/18723 | 2.44e-04 | 4.17e-03 | 22 |
GO:00346141 | Colorectum | SER | cellular response to reactive oxygen species | 41/2897 | 155/18723 | 2.89e-04 | 4.74e-03 | 41 |
GO:00974211 | Colorectum | SER | liver regeneration | 14/2897 | 35/18723 | 4.02e-04 | 6.02e-03 | 14 |
GO:00466861 | Colorectum | SER | response to cadmium ion | 21/2897 | 68/18723 | 1.05e-03 | 1.22e-02 | 21 |
GO:00320701 | Colorectum | SER | regulation of deoxyribonuclease activity | 6/2897 | 10/18723 | 1.63e-03 | 1.72e-02 | 6 |
GO:00718971 | Colorectum | SER | DNA biosynthetic process | 43/2897 | 180/18723 | 1.99e-03 | 1.98e-02 | 43 |
GO:00485111 | Colorectum | SER | rhythmic process | 65/2897 | 298/18723 | 2.18e-03 | 2.11e-02 | 65 |
GO:20010201 | Colorectum | SER | regulation of response to DNA damage stimulus | 49/2897 | 219/18723 | 4.24e-03 | 3.45e-02 | 49 |
GO:00007231 | Colorectum | SER | telomere maintenance | 32/2897 | 131/18723 | 4.90e-03 | 3.82e-02 | 32 |
GO:19016541 | Colorectum | SER | response to ketone | 44/2897 | 194/18723 | 5.01e-03 | 3.88e-02 | 44 |
GO:00487322 | Colorectum | MSS | gland development | 143/3467 | 436/18723 | 3.85e-13 | 8.01e-11 | 143 |
GO:00510522 | Colorectum | MSS | regulation of DNA metabolic process | 108/3467 | 359/18723 | 5.86e-08 | 3.10e-06 | 108 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0453018 | Breast | Precancer | Tight junction | 31/684 | 169/8465 | 1.13e-05 | 1.26e-04 | 9.64e-05 | 31 |
hsa0453019 | Breast | Precancer | Tight junction | 31/684 | 169/8465 | 1.13e-05 | 1.26e-04 | 9.64e-05 | 31 |
hsa0453024 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
hsa0453034 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
hsa0453044 | Breast | DCIS | Tight junction | 37/846 | 169/8465 | 3.07e-06 | 4.20e-05 | 3.09e-05 | 37 |
hsa0453054 | Breast | DCIS | Tight junction | 37/846 | 169/8465 | 3.07e-06 | 4.20e-05 | 3.09e-05 | 37 |
hsa0453020 | Cervix | CC | Tight junction | 49/1267 | 169/8465 | 1.87e-06 | 1.78e-05 | 1.05e-05 | 49 |
hsa041106 | Cervix | CC | Cell cycle | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
hsa04530110 | Cervix | CC | Tight junction | 49/1267 | 169/8465 | 1.87e-06 | 1.78e-05 | 1.05e-05 | 49 |
hsa0411013 | Cervix | CC | Cell cycle | 36/1267 | 157/8465 | 4.94e-03 | 1.67e-02 | 9.86e-03 | 36 |
hsa04530 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
hsa045301 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
hsa045302 | Colorectum | SER | Tight junction | 59/1580 | 169/8465 | 3.24e-07 | 5.98e-06 | 4.34e-06 | 59 |
hsa045303 | Colorectum | SER | Tight junction | 59/1580 | 169/8465 | 3.24e-07 | 5.98e-06 | 4.34e-06 | 59 |
hsa045304 | Colorectum | MSS | Tight junction | 66/1875 | 169/8465 | 4.10e-07 | 6.25e-06 | 3.83e-06 | 66 |
hsa05161 | Colorectum | MSS | Hepatitis B | 48/1875 | 162/8465 | 1.53e-02 | 4.93e-02 | 3.02e-02 | 48 |
hsa045305 | Colorectum | MSS | Tight junction | 66/1875 | 169/8465 | 4.10e-07 | 6.25e-06 | 3.83e-06 | 66 |
hsa051611 | Colorectum | MSS | Hepatitis B | 48/1875 | 162/8465 | 1.53e-02 | 4.93e-02 | 3.02e-02 | 48 |
hsa045306 | Colorectum | MSI-H | Tight junction | 31/797 | 169/8465 | 2.08e-04 | 2.80e-03 | 2.35e-03 | 31 |
hsa045307 | Colorectum | MSI-H | Tight junction | 31/797 | 169/8465 | 2.08e-04 | 2.80e-03 | 2.35e-03 | 31 |
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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 |
PCNA | SNV | Missense_Mutation | novel | c.7N>C | p.Glu3Gln | p.E3Q | P12004 | protein_coding | deleterious(0.01) | probably_damaging(0.993) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
PCNA | SNV | Missense_Mutation | novel | c.199N>C | p.Ala67Pro | p.A67P | P12004 | protein_coding | tolerated(0.21) | benign(0.432) | TCGA-VS-A953-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | PD |
PCNA | SNV | Missense_Mutation | c.581N>T | p.Ala194Val | p.A194V | P12004 | protein_coding | tolerated(0.1) | benign(0.344) | TCGA-AA-3688-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
PCNA | SNV | Missense_Mutation | c.256G>T | p.Asp86Tyr | p.D86Y | P12004 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
PCNA | SNV | Missense_Mutation | c.208G>A | p.Val70Met | p.V70M | P12004 | protein_coding | tolerated(0.84) | benign(0.053) | TCGA-NH-A5IV-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PCNA | SNV | Missense_Mutation | c.506N>G | p.Phe169Cys | p.F169C | P12004 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AG-3999-01 | Colorectum | rectum adenocarcinoma | Female | <65 | III/IV | Unspecific | PD | ||
PCNA | SNV | Missense_Mutation | c.731T>G | p.Met244Arg | p.M244R | P12004 | protein_coding | tolerated(0.21) | possibly_damaging(0.881) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
PCNA | SNV | Missense_Mutation | novel | c.385N>T | p.Pro129Ser | p.P129S | P12004 | protein_coding | deleterious(0) | possibly_damaging(0.541) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
PCNA | SNV | Missense_Mutation | novel | c.536A>G | p.Asn179Ser | p.N179S | P12004 | protein_coding | tolerated(0.6) | benign(0.015) | TCGA-AJ-A5DW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PCNA | SNV | Missense_Mutation | c.109C>A | p.Leu37Met | p.L37M | P12004 | protein_coding | deleterious(0.05) | probably_damaging(0.936) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | 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 |
5111 | PCNA | NA | ATX-101 | DEOXYCHOLIC ACID | ||
5111 | PCNA | NA | VIT-100 | |||
5111 | PCNA | NA | CAPSAICIN | CAPSAICIN | 9435579 | |
5111 | PCNA | NA | PENTOXIFYLLINE | PENTOXIFYLLINE | 10707869 | |
5111 | PCNA | NA | SUNSCREEN | 17021352 |
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