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Gene: PAK3 |
Gene summary for PAK3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | PAK3 | Gene ID | 5063 |
| Gene name | p21 (RAC1) activated kinase 3 | |
| Gene Alias | ARA | |
| Cytomap | Xq23 | |
| Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | B2RCU6 |
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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 |
| 5063 | PAK3 | HCC1 | Human | Liver | HCC | 1.01e-10 | 1.70e+00 | 0.5336 |
| 5063 | PAK3 | HCC2 | Human | Liver | HCC | 2.35e-25 | 2.06e+00 | 0.5341 |
| 5063 | PAK3 | HCC5 | Human | Liver | HCC | 6.24e-09 | 1.61e+00 | 0.4932 |
| 5063 | PAK3 | S029 | Human | Liver | HCC | 2.88e-02 | 3.13e-01 | 0.2581 |
| 5063 | PAK3 | HTA12-15-2 | Human | Pancreas | PDAC | 2.77e-03 | 8.53e-01 | 0.2315 |
| 5063 | PAK3 | HTA12-23-1 | Human | Pancreas | PDAC | 3.69e-13 | 1.38e+00 | 0.3405 |
| 5063 | PAK3 | HTA12-25-1 | Human | Pancreas | PDAC | 2.32e-08 | 1.05e+00 | 0.313 |
| 5063 | PAK3 | HTA12-26-1 | Human | Pancreas | PDAC | 1.92e-26 | 1.28e+00 | 0.3728 |
| 5063 | PAK3 | HTA12-29-1 | Human | Pancreas | PDAC | 2.72e-58 | 1.27e+00 | 0.3722 |
| 5063 | PAK3 | male-WTA | Human | Thyroid | PTC | 6.98e-04 | 1.42e-02 | 0.1037 |
| 5063 | PAK3 | PTC04 | Human | Thyroid | PTC | 2.37e-04 | 1.21e-01 | 0.1927 |
| 5063 | PAK3 | PTC06 | Human | Thyroid | PTC | 2.56e-05 | 1.00e-01 | 0.2057 |
| 5063 | PAK3 | PTC07 | Human | Thyroid | PTC | 9.77e-04 | -9.68e-03 | 0.2044 |
| 5063 | PAK3 | ATC3 | Human | Thyroid | ATC | 1.13e-04 | 2.21e-01 | 0.338 |
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| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| 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:005076922 | Thyroid | ATC | positive regulation of neurogenesis | 112/6293 | 225/18723 | 3.53e-07 | 5.21e-06 | 112 |
| GO:005076723 | Thyroid | ATC | regulation of neurogenesis | 168/6293 | 364/18723 | 3.73e-07 | 5.48e-06 | 168 |
| GO:0016358110 | Thyroid | ATC | dendrite development | 119/6293 | 243/18723 | 4.65e-07 | 6.75e-06 | 119 |
| GO:005140227 | Thyroid | ATC | neuron apoptotic process | 120/6293 | 246/18723 | 5.41e-07 | 7.75e-06 | 120 |
| GO:006099623 | Thyroid | ATC | dendritic spine development | 57/6293 | 99/18723 | 8.24e-07 | 1.09e-05 | 57 |
| GO:001076116 | Thyroid | ATC | fibroblast migration | 32/6293 | 47/18723 | 1.42e-06 | 1.77e-05 | 32 |
| GO:007189723 | Thyroid | ATC | DNA biosynthetic process | 91/6293 | 180/18723 | 1.84e-06 | 2.24e-05 | 91 |
| GO:005077011 | Thyroid | ATC | regulation of axonogenesis | 80/6293 | 154/18723 | 1.95e-06 | 2.34e-05 | 80 |
| GO:004352323 | Thyroid | ATC | regulation of neuron apoptotic process | 104/6293 | 212/18723 | 2.16e-06 | 2.58e-05 | 104 |
| GO:004352524 | Thyroid | ATC | positive regulation of neuron apoptotic process | 37/6293 | 58/18723 | 2.46e-06 | 2.89e-05 | 37 |
| GO:005196014 | Thyroid | ATC | regulation of nervous system development | 195/6293 | 443/18723 | 2.62e-06 | 3.06e-05 | 195 |
| GO:001077023 | Thyroid | ATC | positive regulation of cell morphogenesis involved in differentiation | 46/6293 | 79/18723 | 6.09e-06 | 6.38e-05 | 46 |
| GO:001097614 | Thyroid | ATC | positive regulation of neuron projection development | 82/6293 | 163/18723 | 7.43e-06 | 7.61e-05 | 82 |
| GO:005196221 | Thyroid | ATC | positive regulation of nervous system development | 126/6293 | 272/18723 | 8.17e-06 | 8.27e-05 | 126 |
| GO:200057325 | Thyroid | ATC | positive regulation of DNA biosynthetic process | 39/6293 | 66/18723 | 1.90e-05 | 1.73e-04 | 39 |
| GO:006099815 | Thyroid | ATC | regulation of dendritic spine development | 36/6293 | 61/18723 | 4.10e-05 | 3.32e-04 | 36 |
| GO:010602716 | Thyroid | ATC | neuron projection organization | 50/6293 | 93/18723 | 4.87e-05 | 3.88e-04 | 50 |
| GO:000283123 | Thyroid | ATC | regulation of response to biotic stimulus | 144/6293 | 327/18723 | 4.94e-05 | 3.91e-04 | 144 |
| GO:004881315 | Thyroid | ATC | dendrite morphogenesis | 71/6293 | 146/18723 | 1.18e-04 | 8.38e-04 | 71 |
| GO:009706115 | Thyroid | ATC | dendritic spine organization | 45/6293 | 84/18723 | 1.27e-04 | 9.03e-04 | 45 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0513242 | Liver | HCC | Salmonella infection | 178/4020 | 249/8465 | 5.90e-15 | 1.98e-13 | 1.10e-13 | 178 |
| hsa0513042 | Liver | HCC | Pathogenic Escherichia coli infection | 129/4020 | 197/8465 | 2.02e-07 | 2.50e-06 | 1.39e-06 | 129 |
| hsa0521121 | Liver | HCC | Renal cell carcinoma | 51/4020 | 69/8465 | 6.76e-06 | 5.53e-05 | 3.07e-05 | 51 |
| hsa0451041 | Liver | HCC | Focal adhesion | 125/4020 | 203/8465 | 3.12e-05 | 1.88e-04 | 1.04e-04 | 125 |
| hsa051709 | Liver | HCC | Human immunodeficiency virus 1 infection | 125/4020 | 212/8465 | 4.51e-04 | 1.94e-03 | 1.08e-03 | 125 |
| hsa040128 | Liver | HCC | ErbB signaling pathway | 54/4020 | 85/8465 | 2.02e-03 | 7.07e-03 | 3.93e-03 | 54 |
| hsa0513252 | Liver | HCC | Salmonella infection | 178/4020 | 249/8465 | 5.90e-15 | 1.98e-13 | 1.10e-13 | 178 |
| hsa0513052 | Liver | HCC | Pathogenic Escherichia coli infection | 129/4020 | 197/8465 | 2.02e-07 | 2.50e-06 | 1.39e-06 | 129 |
| hsa0521131 | Liver | HCC | Renal cell carcinoma | 51/4020 | 69/8465 | 6.76e-06 | 5.53e-05 | 3.07e-05 | 51 |
| hsa0451051 | Liver | HCC | Focal adhesion | 125/4020 | 203/8465 | 3.12e-05 | 1.88e-04 | 1.04e-04 | 125 |
| hsa0517012 | Liver | HCC | Human immunodeficiency virus 1 infection | 125/4020 | 212/8465 | 4.51e-04 | 1.94e-03 | 1.08e-03 | 125 |
| hsa0401211 | Liver | HCC | ErbB signaling pathway | 54/4020 | 85/8465 | 2.02e-03 | 7.07e-03 | 3.93e-03 | 54 |
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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. |
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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 |
| PAK3 | SNV | Missense_Mutation | c.1569N>C | p.Arg523Ser | p.R523S | O75914 | protein_coding | tolerated(0.14) | benign(0.006) | TCGA-A2-A04P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxol | PD | |
| PAK3 | SNV | Missense_Mutation | c.743N>T | p.Ser248Leu | p.S248L | O75914 | protein_coding | tolerated(0.38) | benign(0) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| PAK3 | SNV | Missense_Mutation | novel | c.328N>A | p.Glu110Lys | p.E110K | O75914 | protein_coding | tolerated_low_confidence(0.56) | possibly_damaging(0.828) | TCGA-C8-A3M7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
| PAK3 | SNV | Missense_Mutation | c.145N>T | p.Arg49Cys | p.R49C | O75914 | protein_coding | tolerated(0.18) | possibly_damaging(0.827) | TCGA-E2-A1B0-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | SD | |
| PAK3 | SNV | Missense_Mutation | novel | c.1400N>A | p.Pro467His | p.P467H | O75914 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| PAK3 | SNV | Missense_Mutation | c.649N>C | p.Glu217Gln | p.E217Q | O75914 | protein_coding | tolerated(0.49) | benign(0.358) | TCGA-BI-A0VS-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| PAK3 | SNV | Missense_Mutation | c.823C>T | p.Arg275Trp | p.R275W | O75914 | protein_coding | deleterious(0) | probably_damaging(0.944) | TCGA-C5-A902-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD | |
| PAK3 | SNV | Missense_Mutation | novel | c.1348N>T | p.Pro450Ser | p.P450S | O75914 | protein_coding | tolerated(0.06) | benign(0.221) | TCGA-VS-A9UZ-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
| PAK3 | SNV | Missense_Mutation | rs764106735 | c.654N>T | p.Glu218Asp | p.E218D | O75914 | protein_coding | tolerated(0.56) | benign(0) | TCGA-5M-AAT4-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
| PAK3 | SNV | Missense_Mutation | c.834N>C | p.Lys278Asn | p.K278N | O75914 | protein_coding | deleterious(0.03) | benign(0.099) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=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 |
| 5063 | PAK3 | ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | 310264720 | ||
| 5063 | PAK3 | ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | 310264719 | ||
| 5063 | PAK3 | ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | HESPERADIN | HESPERADIN | 19035792 |
| 5063 | PAK3 | ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | 310264722 | ||
| 5063 | PAK3 | ENZYME, KINASE, SERINE THREONINE KINASE, DRUGGABLE GENOME, CLINICALLY ACTIONABLE | inhibitor | 310264718 | PF-03758309 |
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