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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. |
∗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:000806423 | Thyroid | PTC | regulation of actin polymerization or depolymerization | 98/5968 | 188/18723 | 6.00e-09 | 1.53e-07 | 98 |
GO:003004125 | Thyroid | PTC | actin filament polymerization | 99/5968 | 191/18723 | 7.40e-09 | 1.85e-07 | 99 |
GO:003083220 | Thyroid | PTC | regulation of actin filament length | 98/5968 | 189/18723 | 8.58e-09 | 2.10e-07 | 98 |
GO:006099616 | Thyroid | PTC | dendritic spine development | 59/5968 | 99/18723 | 1.18e-08 | 2.83e-07 | 59 |
GO:1901216113 | Thyroid | PTC | positive regulation of neuron death | 58/5968 | 97/18723 | 1.32e-08 | 3.11e-07 | 58 |
GO:0010769111 | Thyroid | PTC | regulation of cell morphogenesis involved in differentiation | 57/5968 | 96/18723 | 2.50e-08 | 5.62e-07 | 57 |
GO:0051402112 | Thyroid | PTC | neuron apoptotic process | 118/5968 | 246/18723 | 8.99e-08 | 1.81e-06 | 118 |
GO:005105420 | Thyroid | PTC | positive regulation of DNA metabolic process | 100/5968 | 201/18723 | 9.18e-08 | 1.84e-06 | 100 |
GO:0010975110 | Thyroid | PTC | regulation of neuron projection development | 194/5968 | 445/18723 | 1.05e-07 | 2.08e-06 | 194 |
GO:003083326 | Thyroid | PTC | regulation of actin filament polymerization | 88/5968 | 172/18723 | 1.07e-07 | 2.11e-06 | 88 |
GO:001072018 | Thyroid | PTC | positive regulation of cell development | 138/5968 | 298/18723 | 1.13e-07 | 2.22e-06 | 138 |
GO:0010770111 | Thyroid | PTC | positive regulation of cell morphogenesis involved in differentiation | 48/5968 | 79/18723 | 1.15e-07 | 2.26e-06 | 48 |
GO:001635819 | Thyroid | PTC | dendrite development | 115/5968 | 243/18723 | 3.16e-07 | 5.35e-06 | 115 |
GO:006156419 | Thyroid | PTC | axon development | 199/5968 | 467/18723 | 5.27e-07 | 8.53e-06 | 199 |
GO:0043523110 | Thyroid | PTC | regulation of neuron apoptotic process | 102/5968 | 212/18723 | 5.45e-07 | 8.76e-06 | 102 |
GO:000740918 | Thyroid | PTC | axonogenesis | 178/5968 | 418/18723 | 2.17e-06 | 2.91e-05 | 178 |
GO:005076914 | Thyroid | PTC | positive regulation of neurogenesis | 105/5968 | 225/18723 | 2.28e-06 | 3.05e-05 | 105 |
GO:0001667112 | Thyroid | PTC | ameboidal-type cell migration | 198/5968 | 475/18723 | 3.36e-06 | 4.34e-05 | 198 |
GO:00609988 | Thyroid | PTC | regulation of dendritic spine development | 37/5968 | 61/18723 | 3.41e-06 | 4.40e-05 | 37 |
GO:010602715 | Thyroid | PTC | neuron projection organization | 51/5968 | 93/18723 | 3.76e-06 | 4.75e-05 | 51 |
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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 |
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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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