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Gene: PDHB |
Gene summary for PDHB |
Gene summary. |
Gene information | Species | Human | Gene symbol | PDHB | Gene ID | 5162 |
Gene name | pyruvate dehydrogenase E1 subunit beta | |
Gene Alias | PDHBD | |
Cytomap | 3p14.3 | |
Gene Type | protein-coding | GO ID | GO:0005975 | UniProtAcc | P11177 |
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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 |
5162 | PDHB | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.41e-04 | 7.03e-02 | 0.0155 |
5162 | PDHB | HTA11_1938_2000001011 | Human | Colorectum | AD | 3.25e-08 | 3.81e-01 | -0.0811 |
5162 | PDHB | HTA11_78_2000001011 | Human | Colorectum | AD | 2.53e-09 | 2.77e-01 | -0.1088 |
5162 | PDHB | HTA11_347_2000001011 | Human | Colorectum | AD | 4.81e-15 | 3.41e-01 | -0.1954 |
5162 | PDHB | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.26e-12 | 3.44e-01 | -0.059 |
5162 | PDHB | HTA11_2992_2000001011 | Human | Colorectum | SER | 6.20e-04 | 3.56e-01 | -0.1706 |
5162 | PDHB | HTA11_546_2000001011 | Human | Colorectum | AD | 2.85e-03 | 1.37e-01 | -0.0842 |
5162 | PDHB | HTA11_866_3004761011 | Human | Colorectum | AD | 3.84e-06 | 2.11e-01 | 0.096 |
5162 | PDHB | HTA11_6801_2000001011 | Human | Colorectum | SER | 5.10e-03 | 3.61e-01 | 0.0171 |
5162 | PDHB | HTA11_7696_3000711011 | Human | Colorectum | AD | 8.86e-03 | 1.29e-01 | 0.0674 |
5162 | PDHB | HTA11_99999970781_79442 | Human | Colorectum | MSS | 4.83e-08 | 3.83e-01 | 0.294 |
5162 | PDHB | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.37e-06 | 7.79e-01 | 0.3487 |
5162 | PDHB | HTA11_99999965104_69814 | Human | Colorectum | MSS | 7.29e-06 | 2.41e-01 | 0.281 |
5162 | PDHB | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.22e-08 | 3.52e-01 | 0.3859 |
5162 | PDHB | LZE4T | Human | Esophagus | ESCC | 2.46e-13 | 2.51e-01 | 0.0811 |
5162 | PDHB | LZE8T | Human | Esophagus | ESCC | 1.99e-05 | 8.24e-02 | 0.067 |
5162 | PDHB | LZE20T | Human | Esophagus | ESCC | 3.77e-02 | -5.29e-02 | 0.0662 |
5162 | PDHB | LZE22T | Human | Esophagus | ESCC | 1.13e-04 | 1.36e-01 | 0.068 |
5162 | PDHB | LZE24T | Human | Esophagus | ESCC | 4.27e-17 | 3.40e-01 | 0.0596 |
5162 | PDHB | LZE6T | Human | Esophagus | ESCC | 4.24e-04 | 6.32e-02 | 0.0845 |
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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:0072521110 | Oral cavity | LP | purine-containing compound metabolic process | 130/4623 | 416/18723 | 1.30e-03 | 1.05e-02 | 130 |
GO:004639018 | Oral cavity | LP | ribose phosphate biosynthetic process | 65/4623 | 190/18723 | 1.97e-03 | 1.47e-02 | 65 |
GO:190129315 | Oral cavity | LP | nucleoside phosphate biosynthetic process | 84/4623 | 256/18723 | 1.98e-03 | 1.47e-02 | 84 |
GO:0009259110 | Oral cavity | LP | ribonucleotide metabolic process | 120/4623 | 385/18723 | 2.15e-03 | 1.57e-02 | 120 |
GO:000916515 | Oral cavity | LP | nucleotide biosynthetic process | 83/4623 | 254/18723 | 2.38e-03 | 1.71e-02 | 83 |
GO:001931813 | Oral cavity | LP | hexose metabolic process | 78/4623 | 237/18723 | 2.55e-03 | 1.80e-02 | 78 |
GO:0006163110 | Oral cavity | LP | purine nucleotide metabolic process | 122/4623 | 396/18723 | 3.10e-03 | 2.11e-02 | 122 |
GO:000679012 | Oral cavity | LP | sulfur compound metabolic process | 106/4623 | 339/18723 | 3.36e-03 | 2.25e-02 | 106 |
GO:0009150110 | Oral cavity | LP | purine ribonucleotide metabolic process | 114/4623 | 368/18723 | 3.41e-03 | 2.28e-02 | 114 |
GO:007252210 | Oral cavity | LP | purine-containing compound biosynthetic process | 66/4623 | 200/18723 | 4.84e-03 | 3.05e-02 | 66 |
GO:000600614 | Oral cavity | LP | glucose metabolic process | 64/4623 | 196/18723 | 7.09e-03 | 3.98e-02 | 64 |
GO:000926018 | Oral cavity | LP | ribonucleotide biosynthetic process | 60/4623 | 182/18723 | 7.12e-03 | 4.00e-02 | 60 |
GO:000616410 | Oral cavity | LP | purine nucleotide biosynthetic process | 62/4623 | 191/18723 | 9.12e-03 | 4.86e-02 | 62 |
GO:0009060111 | Skin | cSCC | aerobic respiration | 118/4864 | 189/18723 | 3.71e-26 | 1.22e-23 | 118 |
GO:0045333111 | Skin | cSCC | cellular respiration | 131/4864 | 230/18723 | 1.57e-23 | 3.39e-21 | 131 |
GO:0006091111 | Skin | cSCC | generation of precursor metabolites and energy | 224/4864 | 490/18723 | 1.13e-21 | 2.21e-19 | 224 |
GO:001598026 | Skin | cSCC | energy derivation by oxidation of organic compounds | 154/4864 | 318/18723 | 4.19e-18 | 5.15e-16 | 154 |
GO:00060998 | Skin | cSCC | tricarboxylic acid cycle | 22/4864 | 30/18723 | 7.72e-08 | 1.90e-06 | 22 |
GO:0019693112 | Skin | cSCC | ribose phosphate metabolic process | 146/4864 | 396/18723 | 9.28e-07 | 1.68e-05 | 146 |
GO:000675324 | Skin | cSCC | nucleoside phosphate metabolic process | 176/4864 | 497/18723 | 1.55e-06 | 2.62e-05 | 176 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05415 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
hsa01200 | Colorectum | AD | Carbon metabolism | 55/2092 | 115/8465 | 5.53e-08 | 8.42e-07 | 5.37e-07 | 55 |
hsa00620 | Colorectum | AD | Pyruvate metabolism | 28/2092 | 47/8465 | 3.71e-07 | 5.41e-06 | 3.45e-06 | 28 |
hsa00020 | Colorectum | AD | Citrate cycle (TCA cycle) | 20/2092 | 30/8465 | 1.43e-06 | 1.77e-05 | 1.13e-05 | 20 |
hsa00010 | Colorectum | AD | Glycolysis / Gluconeogenesis | 34/2092 | 67/8465 | 3.63e-06 | 4.34e-05 | 2.77e-05 | 34 |
hsa04066 | Colorectum | AD | HIF-1 signaling pathway | 48/2092 | 109/8465 | 7.25e-06 | 7.84e-05 | 5.00e-05 | 48 |
hsa05230 | Colorectum | AD | Central carbon metabolism in cancer | 33/2092 | 70/8465 | 3.61e-05 | 3.19e-04 | 2.03e-04 | 33 |
hsa04922 | Colorectum | AD | Glucagon signaling pathway | 41/2092 | 107/8465 | 1.18e-03 | 7.75e-03 | 4.94e-03 | 41 |
hsa054151 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
hsa012001 | Colorectum | AD | Carbon metabolism | 55/2092 | 115/8465 | 5.53e-08 | 8.42e-07 | 5.37e-07 | 55 |
hsa006201 | Colorectum | AD | Pyruvate metabolism | 28/2092 | 47/8465 | 3.71e-07 | 5.41e-06 | 3.45e-06 | 28 |
hsa000201 | Colorectum | AD | Citrate cycle (TCA cycle) | 20/2092 | 30/8465 | 1.43e-06 | 1.77e-05 | 1.13e-05 | 20 |
hsa000101 | Colorectum | AD | Glycolysis / Gluconeogenesis | 34/2092 | 67/8465 | 3.63e-06 | 4.34e-05 | 2.77e-05 | 34 |
hsa040661 | Colorectum | AD | HIF-1 signaling pathway | 48/2092 | 109/8465 | 7.25e-06 | 7.84e-05 | 5.00e-05 | 48 |
hsa052301 | Colorectum | AD | Central carbon metabolism in cancer | 33/2092 | 70/8465 | 3.61e-05 | 3.19e-04 | 2.03e-04 | 33 |
hsa049221 | Colorectum | AD | Glucagon signaling pathway | 41/2092 | 107/8465 | 1.18e-03 | 7.75e-03 | 4.94e-03 | 41 |
hsa054152 | Colorectum | SER | Diabetic cardiomyopathy | 103/1580 | 203/8465 | 1.45e-25 | 1.61e-23 | 1.17e-23 | 103 |
hsa006202 | Colorectum | SER | Pyruvate metabolism | 22/1580 | 47/8465 | 9.62e-06 | 1.33e-04 | 9.67e-05 | 22 |
hsa000202 | Colorectum | SER | Citrate cycle (TCA cycle) | 16/1580 | 30/8465 | 2.06e-05 | 2.74e-04 | 1.99e-04 | 16 |
hsa049222 | Colorectum | SER | Glucagon signaling pathway | 38/1580 | 107/8465 | 2.57e-05 | 3.28e-04 | 2.38e-04 | 38 |
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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 |
PDHB | SNV | Missense_Mutation | novel | c.947N>C | p.Asn316Thr | p.N316T | P11177 | protein_coding | deleterious(0.01) | benign(0.259) | TCGA-E2-A15A-06 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD |
PDHB | SNV | Missense_Mutation | c.985G>A | p.Asp329Asn | p.D329N | P11177 | protein_coding | deleterious(0.01) | probably_damaging(0.942) | TCGA-IR-A3LA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
PDHB | SNV | Missense_Mutation | novel | c.445N>A | p.Gly149Ser | p.G149S | P11177 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-AA-3845-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
PDHB | SNV | Missense_Mutation | novel | c.959N>T | p.Ala320Val | p.A320V | P11177 | protein_coding | deleterious(0) | possibly_damaging(0.829) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PDHB | SNV | Missense_Mutation | c.157N>A | p.Val53Ile | p.V53I | P11177 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-AA-A00N-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
PDHB | SNV | Missense_Mutation | novel | c.787N>C | p.Cys263Arg | p.C263R | P11177 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-CA-6717-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Chemotherapy | oxaliplatin | CR |
PDHB | SNV | Missense_Mutation | c.794N>C | p.Val265Ala | p.V265A | P11177 | protein_coding | deleterious(0) | probably_damaging(0.978) | TCGA-A5-A0GW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
PDHB | SNV | Missense_Mutation | novel | c.839N>C | p.Glu280Ala | p.E280A | P11177 | protein_coding | tolerated(0.33) | benign(0.019) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PDHB | SNV | Missense_Mutation | novel | c.970N>T | p.Arg324Cys | p.R324C | P11177 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PDHB | SNV | Missense_Mutation | novel | c.345N>A | p.Phe115Leu | p.F115L | P11177 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AJ-A3EL-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 |
5162 | PDHB | ENZYME | CPI-613 | |||
5162 | PDHB | ENZYME | DEXLIPOTAM |
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