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Gene: PDK4 |
Gene summary for PDK4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | PDK4 | Gene ID | 5166 |
Gene name | pyruvate dehydrogenase kinase 4 | |
Gene Alias | PDK4 | |
Cytomap | 7q21.3 | |
Gene Type | protein-coding | GO ID | GO:0001894 | UniProtAcc | A4D1H4 |
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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 |
5166 | PDK4 | GSM4909280 | Human | Breast | Precancer | 1.02e-04 | 5.73e-01 | 0.0305 |
5166 | PDK4 | GSM4909281 | Human | Breast | IDC | 5.37e-03 | -1.67e-01 | 0.21 |
5166 | PDK4 | GSM4909282 | Human | Breast | IDC | 3.66e-05 | -1.72e-01 | -0.0288 |
5166 | PDK4 | GSM4909285 | Human | Breast | IDC | 3.66e-05 | -1.72e-01 | 0.21 |
5166 | PDK4 | GSM4909286 | Human | Breast | IDC | 1.72e-05 | -1.74e-01 | 0.1081 |
5166 | PDK4 | GSM4909290 | Human | Breast | IDC | 5.07e-03 | -1.74e-01 | 0.2096 |
5166 | PDK4 | GSM4909296 | Human | Breast | IDC | 1.64e-03 | -1.56e-01 | 0.1524 |
5166 | PDK4 | GSM4909311 | Human | Breast | IDC | 1.15e-04 | -1.24e-01 | 0.1534 |
5166 | PDK4 | GSM4909315 | Human | Breast | IDC | 1.72e-05 | -1.74e-01 | 0.21 |
5166 | PDK4 | GSM4909319 | Human | Breast | IDC | 1.47e-08 | 1.42e-02 | 0.1563 |
5166 | PDK4 | brca2 | Human | Breast | Precancer | 1.09e-03 | 2.44e-01 | -0.024 |
5166 | PDK4 | NCCBC5 | Human | Breast | DCIS | 2.81e-03 | -1.74e-01 | 0.2046 |
5166 | PDK4 | DCIS2 | Human | Breast | DCIS | 1.66e-30 | 5.89e-01 | 0.0085 |
5166 | PDK4 | NAFLD1 | Human | Liver | NAFLD | 2.30e-02 | 4.03e-01 | -0.04 |
5166 | PDK4 | S43 | Human | Liver | Cirrhotic | 9.81e-08 | 1.57e-01 | -0.0187 |
5166 | PDK4 | S44 | Human | Liver | HCC | 3.51e-23 | 1.73e+00 | -0.0083 |
5166 | PDK4 | HCC1_Meng | Human | Liver | HCC | 4.47e-04 | -1.99e-01 | 0.0246 |
5166 | PDK4 | HCC2_Meng | Human | Liver | HCC | 4.09e-14 | 2.06e-03 | 0.0107 |
5166 | PDK4 | HCC1 | Human | Liver | HCC | 9.06e-05 | 2.46e+00 | 0.5336 |
5166 | PDK4 | HCC2 | Human | Liver | HCC | 1.26e-04 | 2.96e+00 | 0.5341 |
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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:0034033 | Liver | Cirrhotic | purine nucleoside bisphosphate biosynthetic process | 25/4634 | 60/18723 | 2.92e-03 | 1.67e-02 | 25 |
GO:19005423 | Liver | Cirrhotic | regulation of purine nucleotide metabolic process | 32/4634 | 84/18723 | 4.53e-03 | 2.40e-02 | 32 |
GO:0006085 | Liver | Cirrhotic | acetyl-CoA biosynthetic process | 10/4634 | 18/18723 | 5.00e-03 | 2.59e-02 | 10 |
GO:0035384 | Liver | Cirrhotic | thioester biosynthetic process | 19/4634 | 45/18723 | 7.53e-03 | 3.57e-02 | 19 |
GO:0071616 | Liver | Cirrhotic | acyl-CoA biosynthetic process | 19/4634 | 45/18723 | 7.53e-03 | 3.57e-02 | 19 |
GO:00068853 | Liver | Cirrhotic | regulation of pH | 33/4634 | 91/18723 | 9.39e-03 | 4.29e-02 | 33 |
GO:00423043 | Liver | Cirrhotic | regulation of fatty acid biosynthetic process | 20/4634 | 49/18723 | 9.60e-03 | 4.35e-02 | 20 |
GO:000911722 | Liver | HCC | nucleotide metabolic process | 300/7958 | 489/18723 | 1.61e-17 | 1.71e-15 | 300 |
GO:000675322 | Liver | HCC | nucleoside phosphate metabolic process | 304/7958 | 497/18723 | 1.78e-17 | 1.85e-15 | 304 |
GO:001969322 | Liver | HCC | ribose phosphate metabolic process | 248/7958 | 396/18723 | 3.15e-16 | 2.70e-14 | 248 |
GO:000925922 | Liver | HCC | ribonucleotide metabolic process | 240/7958 | 385/18723 | 2.07e-15 | 1.51e-13 | 240 |
GO:001605321 | Liver | HCC | organic acid biosynthetic process | 200/7958 | 316/18723 | 5.24e-14 | 3.22e-12 | 200 |
GO:000679021 | Liver | HCC | sulfur compound metabolic process | 212/7958 | 339/18723 | 5.60e-14 | 3.39e-12 | 212 |
GO:003286821 | Liver | HCC | response to insulin | 172/7958 | 264/18723 | 7.14e-14 | 4.23e-12 | 172 |
GO:000663122 | Liver | HCC | fatty acid metabolic process | 238/7958 | 390/18723 | 8.24e-14 | 4.84e-12 | 238 |
GO:004639421 | Liver | HCC | carboxylic acid biosynthetic process | 198/7958 | 314/18723 | 1.19e-13 | 6.78e-12 | 198 |
GO:000915022 | Liver | HCC | purine ribonucleotide metabolic process | 226/7958 | 368/18723 | 1.36e-13 | 7.69e-12 | 226 |
GO:007252122 | Liver | HCC | purine-containing compound metabolic process | 250/7958 | 416/18723 | 2.26e-13 | 1.24e-11 | 250 |
GO:000599621 | Liver | HCC | monosaccharide metabolic process | 167/7958 | 257/18723 | 2.31e-13 | 1.25e-11 | 167 |
GO:003286921 | Liver | HCC | cellular response to insulin stimulus | 137/7958 | 203/18723 | 4.69e-13 | 2.44e-11 | 137 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0541518 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
hsa0541519 | Breast | Precancer | Diabetic cardiomyopathy | 63/684 | 203/8465 | 5.63e-22 | 1.48e-20 | 1.14e-20 | 63 |
hsa0541523 | Breast | IDC | Diabetic cardiomyopathy | 67/867 | 203/8465 | 3.17e-19 | 8.59e-18 | 6.43e-18 | 67 |
hsa0541533 | Breast | IDC | Diabetic cardiomyopathy | 67/867 | 203/8465 | 3.17e-19 | 8.59e-18 | 6.43e-18 | 67 |
hsa0541543 | Breast | DCIS | Diabetic cardiomyopathy | 65/846 | 203/8465 | 1.81e-18 | 4.87e-17 | 3.59e-17 | 65 |
hsa0541553 | Breast | DCIS | Diabetic cardiomyopathy | 65/846 | 203/8465 | 1.81e-18 | 4.87e-17 | 3.59e-17 | 65 |
hsa0541514 | Liver | Cirrhotic | Diabetic cardiomyopathy | 108/2530 | 203/8465 | 1.99e-12 | 4.41e-11 | 2.72e-11 | 108 |
hsa0541515 | Liver | Cirrhotic | Diabetic cardiomyopathy | 108/2530 | 203/8465 | 1.99e-12 | 4.41e-11 | 2.72e-11 | 108 |
hsa0541522 | Liver | HCC | Diabetic cardiomyopathy | 151/4020 | 203/8465 | 2.72e-15 | 1.01e-13 | 5.63e-14 | 151 |
hsa0541532 | Liver | HCC | Diabetic cardiomyopathy | 151/4020 | 203/8465 | 2.72e-15 | 1.01e-13 | 5.63e-14 | 151 |
hsa0541529 | Oral cavity | OSCC | Diabetic cardiomyopathy | 131/3704 | 203/8465 | 1.33e-09 | 1.49e-08 | 7.57e-09 | 131 |
hsa05415113 | Oral cavity | OSCC | Diabetic cardiomyopathy | 131/3704 | 203/8465 | 1.33e-09 | 1.49e-08 | 7.57e-09 | 131 |
hsa0541527 | Prostate | BPH | Diabetic cardiomyopathy | 102/1718 | 203/8465 | 6.06e-22 | 2.00e-20 | 1.24e-20 | 102 |
hsa05415112 | Prostate | BPH | Diabetic cardiomyopathy | 102/1718 | 203/8465 | 6.06e-22 | 2.00e-20 | 1.24e-20 | 102 |
hsa0541528 | Prostate | Tumor | Diabetic cardiomyopathy | 103/1791 | 203/8465 | 4.04e-21 | 1.22e-19 | 7.54e-20 | 103 |
hsa0541536 | Prostate | Tumor | Diabetic cardiomyopathy | 103/1791 | 203/8465 | 4.04e-21 | 1.22e-19 | 7.54e-20 | 103 |
hsa0541512 | Stomach | GC | Diabetic cardiomyopathy | 56/708 | 203/8465 | 2.48e-16 | 1.14e-14 | 8.00e-15 | 56 |
hsa0541513 | Stomach | GC | Diabetic cardiomyopathy | 56/708 | 203/8465 | 2.48e-16 | 1.14e-14 | 8.00e-15 | 56 |
hsa0541521 | Stomach | CAG with IM | Diabetic cardiomyopathy | 56/640 | 203/8465 | 2.41e-18 | 1.10e-16 | 7.69e-17 | 56 |
hsa0541531 | Stomach | CAG with IM | Diabetic cardiomyopathy | 56/640 | 203/8465 | 2.41e-18 | 1.10e-16 | 7.69e-17 | 56 |
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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 |
PDK4 | SNV | Missense_Mutation | c.1034A>T | p.Gln345Leu | p.Q345L | Q16654 | protein_coding | tolerated(0.07) | benign(0.014) | TCGA-A8-A090-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PDK4 | SNV | Missense_Mutation | c.905N>G | p.Ile302Ser | p.I302S | Q16654 | protein_coding | tolerated(0.07) | benign(0.076) | TCGA-A8-A092-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | CR | |
PDK4 | SNV | Missense_Mutation | c.884G>A | p.Gly295Glu | p.G295E | Q16654 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
PDK4 | SNV | Missense_Mutation | rs778644301 | c.477N>T | p.Leu159Phe | p.L159F | Q16654 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-GI-A2C8-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | Adriamycin | SD |
PDK4 | deletion | Frame_Shift_Del | novel | c.517delN | p.Met173Ter | p.M173* | Q16654 | protein_coding | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | ||
PDK4 | SNV | Missense_Mutation | novel | c.875N>T | p.Ser292Leu | p.S292L | Q16654 | protein_coding | deleterious(0) | probably_damaging(0.989) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
PDK4 | SNV | Missense_Mutation | c.997N>A | p.Gly333Ser | p.G333S | Q16654 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-AA-3864-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
PDK4 | SNV | Missense_Mutation | rs142890516 | c.768N>G | p.Phe256Leu | p.F256L | Q16654 | protein_coding | tolerated(0.21) | benign(0.229) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
PDK4 | SNV | Missense_Mutation | novel | c.680N>G | p.Leu227Arg | p.L227R | Q16654 | protein_coding | deleterious(0) | possibly_damaging(0.747) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
PDK4 | SNV | Missense_Mutation | novel | c.565A>C | p.Ser189Arg | p.S189R | Q16654 | protein_coding | tolerated(0.94) | benign(0) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
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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 |
5166 | PDK4 | DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, ENZYME | CPI-613 | |||
5166 | PDK4 | DRUGGABLE GENOME, SERINE THREONINE KINASE, KINASE, ENZYME | inhibitor | 328083452 |
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