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Gene: PRKCD |
Gene summary for PRKCD |
Gene summary. |
Gene information | Species | Human | Gene symbol | PRKCD | Gene ID | 5580 |
Gene name | protein kinase C delta | |
Gene Alias | ALPS3 | |
Cytomap | 3p21.1 | |
Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | A0A024R328 |
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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 |
5580 | PRKCD | HTA11_2487_2000001011 | Human | Colorectum | SER | 6.51e-20 | 9.21e-01 | -0.1808 |
5580 | PRKCD | HTA11_78_2000001011 | Human | Colorectum | AD | 1.77e-08 | 5.77e-01 | -0.1088 |
5580 | PRKCD | HTA11_347_2000001011 | Human | Colorectum | AD | 5.65e-26 | 7.29e-01 | -0.1954 |
5580 | PRKCD | HTA11_411_2000001011 | Human | Colorectum | SER | 2.14e-03 | 1.16e+00 | -0.2602 |
5580 | PRKCD | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.76e-05 | 8.71e-01 | -0.2196 |
5580 | PRKCD | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.61e-03 | 4.74e-01 | -0.1207 |
5580 | PRKCD | HTA11_83_2000001011 | Human | Colorectum | SER | 1.37e-09 | 6.32e-01 | -0.1526 |
5580 | PRKCD | HTA11_696_2000001011 | Human | Colorectum | AD | 5.27e-22 | 6.28e-01 | -0.1464 |
5580 | PRKCD | HTA11_866_2000001011 | Human | Colorectum | AD | 6.34e-09 | 3.95e-01 | -0.1001 |
5580 | PRKCD | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.87e-09 | 5.71e-01 | -0.059 |
5580 | PRKCD | HTA11_5212_2000001011 | Human | Colorectum | AD | 3.41e-04 | 6.88e-01 | -0.2061 |
5580 | PRKCD | HTA11_866_3004761011 | Human | Colorectum | AD | 1.51e-02 | 3.24e-01 | 0.096 |
5580 | PRKCD | HTA11_7696_3000711011 | Human | Colorectum | AD | 8.99e-08 | 3.38e-01 | 0.0674 |
5580 | PRKCD | HTA11_99999970781_79442 | Human | Colorectum | MSS | 3.80e-03 | 2.58e-01 | 0.294 |
5580 | PRKCD | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.61e-05 | 4.24e-01 | 0.281 |
5580 | PRKCD | HTA11_99999971662_82457 | Human | Colorectum | MSS | 3.32e-11 | 5.38e-01 | 0.3859 |
5580 | PRKCD | LZE8T | Human | Esophagus | ESCC | 4.02e-03 | 8.17e-03 | 0.067 |
5580 | PRKCD | LZE24T | Human | Esophagus | ESCC | 2.48e-17 | 2.78e-01 | 0.0596 |
5580 | PRKCD | LZE21T | Human | Esophagus | ESCC | 2.79e-02 | 1.64e-01 | 0.0655 |
5580 | PRKCD | P1T-E | Human | Esophagus | ESCC | 9.70e-05 | 2.35e-01 | 0.0875 |
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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:000697934 | Thyroid | ATC | response to oxidative stress | 246/6293 | 446/18723 | 2.98e-21 | 6.09e-19 | 246 |
GO:003450423 | Thyroid | ATC | protein localization to nucleus | 175/6293 | 290/18723 | 6.23e-21 | 1.23e-18 | 175 |
GO:000691326 | Thyroid | ATC | nucleocytoplasmic transport | 180/6293 | 301/18723 | 6.97e-21 | 1.30e-18 | 180 |
GO:005116926 | Thyroid | ATC | nuclear transport | 180/6293 | 301/18723 | 6.97e-21 | 1.30e-18 | 180 |
GO:1903829210 | Thyroid | ATC | positive regulation of cellular protein localization | 167/6293 | 276/18723 | 3.32e-20 | 5.38e-18 | 167 |
GO:003164734 | Thyroid | ATC | regulation of protein stability | 177/6293 | 298/18723 | 4.08e-20 | 6.46e-18 | 177 |
GO:003238825 | Thyroid | ATC | positive regulation of intracellular transport | 131/6293 | 202/18723 | 8.20e-20 | 1.24e-17 | 131 |
GO:009719335 | Thyroid | ATC | intrinsic apoptotic signaling pathway | 171/6293 | 288/18723 | 1.86e-19 | 2.67e-17 | 171 |
GO:000640127 | Thyroid | ATC | RNA catabolic process | 165/6293 | 278/18723 | 8.45e-19 | 1.14e-16 | 165 |
GO:005109834 | Thyroid | ATC | regulation of binding | 203/6293 | 363/18723 | 1.18e-18 | 1.55e-16 | 203 |
GO:1902903210 | Thyroid | ATC | regulation of supramolecular fiber organization | 210/6293 | 383/18723 | 6.20e-18 | 7.54e-16 | 210 |
GO:009031624 | Thyroid | ATC | positive regulation of intracellular protein transport | 107/6293 | 160/18723 | 6.82e-18 | 7.84e-16 | 107 |
GO:001657017 | Thyroid | ATC | histone modification | 243/6293 | 463/18723 | 2.23e-17 | 2.27e-15 | 243 |
GO:001056334 | Thyroid | ATC | negative regulation of phosphorus metabolic process | 234/6293 | 442/18723 | 2.30e-17 | 2.31e-15 | 234 |
GO:006219734 | Thyroid | ATC | cellular response to chemical stress | 188/6293 | 337/18723 | 3.16e-17 | 3.07e-15 | 188 |
GO:004593634 | Thyroid | ATC | negative regulation of phosphate metabolic process | 233/6293 | 441/18723 | 3.68e-17 | 3.47e-15 | 233 |
GO:000640227 | Thyroid | ATC | mRNA catabolic process | 140/6293 | 232/18723 | 5.08e-17 | 4.65e-15 | 140 |
GO:003465525 | Thyroid | ATC | nucleobase-containing compound catabolic process | 217/6293 | 407/18723 | 1.20e-16 | 1.04e-14 | 217 |
GO:0043254210 | Thyroid | ATC | regulation of protein-containing complex assembly | 225/6293 | 428/18723 | 2.72e-16 | 2.33e-14 | 225 |
GO:190495128 | Thyroid | ATC | positive regulation of establishment of protein localization | 177/6293 | 319/18723 | 5.43e-16 | 4.29e-14 | 177 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05208 | Colorectum | AD | Chemical carcinogenesis - reactive oxygen species | 126/2092 | 223/8465 | 1.01e-24 | 1.68e-22 | 1.07e-22 | 126 |
hsa05415 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
hsa05020 | Colorectum | AD | Prion disease | 133/2092 | 273/8465 | 2.47e-18 | 8.29e-17 | 5.29e-17 | 133 |
hsa05131 | Colorectum | AD | Shigellosis | 109/2092 | 247/8465 | 1.09e-11 | 2.44e-10 | 1.55e-10 | 109 |
hsa04666 | Colorectum | AD | Fc gamma R-mediated phagocytosis | 46/2092 | 97/8465 | 9.10e-07 | 1.22e-05 | 7.77e-06 | 46 |
hsa04722 | Colorectum | AD | Neurotrophin signaling pathway | 50/2092 | 119/8465 | 2.28e-05 | 2.24e-04 | 1.43e-04 | 50 |
hsa04912 | Colorectum | AD | GnRH signaling pathway | 35/2092 | 93/8465 | 3.69e-03 | 1.90e-02 | 1.21e-02 | 35 |
hsa04140 | Colorectum | AD | Autophagy - animal | 49/2092 | 141/8465 | 4.58e-03 | 2.20e-02 | 1.40e-02 | 49 |
hsa052081 | Colorectum | AD | Chemical carcinogenesis - reactive oxygen species | 126/2092 | 223/8465 | 1.01e-24 | 1.68e-22 | 1.07e-22 | 126 |
hsa054151 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
hsa050201 | Colorectum | AD | Prion disease | 133/2092 | 273/8465 | 2.47e-18 | 8.29e-17 | 5.29e-17 | 133 |
hsa051311 | Colorectum | AD | Shigellosis | 109/2092 | 247/8465 | 1.09e-11 | 2.44e-10 | 1.55e-10 | 109 |
hsa046661 | Colorectum | AD | Fc gamma R-mediated phagocytosis | 46/2092 | 97/8465 | 9.10e-07 | 1.22e-05 | 7.77e-06 | 46 |
hsa047221 | Colorectum | AD | Neurotrophin signaling pathway | 50/2092 | 119/8465 | 2.28e-05 | 2.24e-04 | 1.43e-04 | 50 |
hsa049121 | Colorectum | AD | GnRH signaling pathway | 35/2092 | 93/8465 | 3.69e-03 | 1.90e-02 | 1.21e-02 | 35 |
hsa041401 | Colorectum | AD | Autophagy - animal | 49/2092 | 141/8465 | 4.58e-03 | 2.20e-02 | 1.40e-02 | 49 |
hsa054152 | Colorectum | SER | Diabetic cardiomyopathy | 103/1580 | 203/8465 | 1.45e-25 | 1.61e-23 | 1.17e-23 | 103 |
hsa050202 | Colorectum | SER | Prion disease | 119/1580 | 273/8465 | 4.61e-22 | 3.06e-20 | 2.22e-20 | 119 |
hsa052082 | Colorectum | SER | Chemical carcinogenesis - reactive oxygen species | 103/1580 | 223/8465 | 1.60e-21 | 7.57e-20 | 5.50e-20 | 103 |
hsa051312 | Colorectum | SER | Shigellosis | 87/1580 | 247/8465 | 3.07e-10 | 7.27e-09 | 5.28e-09 | 87 |
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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 |
PRKCD | SNV | Missense_Mutation | novel | c.1115N>T | p.Gly372Val | p.G372V | Q05655 | protein_coding | deleterious(0.01) | benign(0.342) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD |
PRKCD | SNV | Missense_Mutation | novel | c.548A>T | p.Asn183Ile | p.N183I | Q05655 | protein_coding | deleterious(0.03) | probably_damaging(0.985) | TCGA-AN-A0FN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PRKCD | SNV | Missense_Mutation | c.1573N>A | p.Tyr525Asn | p.Y525N | Q05655 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AR-A24K-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD | |
PRKCD | SNV | Missense_Mutation | rs781980599 | c.277N>A | p.Glu93Lys | p.E93K | Q05655 | protein_coding | deleterious(0.02) | benign(0.407) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD |
PRKCD | SNV | Missense_Mutation | novel | c.609N>C | p.Lys203Asn | p.K203N | Q05655 | protein_coding | tolerated(0.21) | possibly_damaging(0.811) | TCGA-D8-A1JA-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | adriamycin | PD |
PRKCD | insertion | Frame_Shift_Ins | novel | c.1528_1529insAGGAGAAGCAGAGGCTGCTC | p.Gly510GlufsTer21 | p.G510Efs*21 | Q05655 | protein_coding | TCGA-AN-A0FT-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
PRKCD | insertion | Frame_Shift_Ins | novel | c.1989_1990insA | p.Ser664IlefsTer22 | p.S664Ifs*22 | Q05655 | protein_coding | TCGA-BH-A0BD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
PRKCD | insertion | Nonsense_Mutation | novel | c.1990_1991insTTTAAAATATAAGTTCAGGCCGGGCACAGTGGC | p.Ser664delinsPheTerAsnIleSerSerGlyArgAlaGlnTrpPro | p.S664delinsF*NISSGRAQWP | Q05655 | protein_coding | TCGA-BH-A0BD-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | ||
PRKCD | SNV | Missense_Mutation | rs149165175 | c.604G>A | p.Asp202Asn | p.D202N | Q05655 | protein_coding | tolerated(0.07) | benign(0.105) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PRKCD | SNV | Missense_Mutation | rs782258819 | c.422N>T | p.Thr141Met | p.T141M | Q05655 | protein_coding | tolerated(0.12) | benign(0.107) | TCGA-EA-A410-01 | Cervix | cervical & endocervical cancer | 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 |
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | TAE-684 | TAE-684 | ||
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | [3H]-PHORBOL 12,13-DIBUTYRATE | CHEMBL27768 | 24794745 | |
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | GO-6976 | GO-6976 | ||
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | ETHANOL | ALCOHOL | 1744136 | |
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | inhibitor | CHEMBL565612 | SOTRASTAURIN | |
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | inhibitor | 178101947 | RUBOXISTAURIN | |
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | ENOXOLONE | ENOXOLONE | 24461294 | |
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | inhibitor | CHEMBL574737 | UCN-01 | |
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | KAI-9803 | DELCASERTIB | ||
5580 | PRKCD | ENZYME, DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, TRANSCRIPTION FACTOR | inhibitor | CHEMBL608533 | MIDOSTAURIN |
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