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Gene: BCKDHB |
Gene summary for BCKDHB |
Gene summary. |
Gene information | Species | Human | Gene symbol | BCKDHB | Gene ID | 594 |
Gene name | branched chain keto acid dehydrogenase E1 subunit beta | |
Gene Alias | BCKDE1B | |
Cytomap | 6q14.1 | |
Gene Type | protein-coding | GO ID | GO:0006082 | UniProtAcc | A0A140VKB3 |
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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 |
594 | BCKDHB | HTA11_3410_2000001011 | Human | Colorectum | AD | 3.38e-09 | -5.14e-01 | 0.0155 |
594 | BCKDHB | HTA11_3361_2000001011 | Human | Colorectum | AD | 4.23e-05 | -5.15e-01 | -0.1207 |
594 | BCKDHB | HTA11_696_2000001011 | Human | Colorectum | AD | 1.73e-03 | -3.09e-01 | -0.1464 |
594 | BCKDHB | HTA11_866_2000001011 | Human | Colorectum | AD | 1.24e-04 | -3.77e-01 | -0.1001 |
594 | BCKDHB | HTA11_866_3004761011 | Human | Colorectum | AD | 3.21e-08 | -5.34e-01 | 0.096 |
594 | BCKDHB | HTA11_7696_3000711011 | Human | Colorectum | AD | 3.61e-03 | -3.41e-01 | 0.0674 |
594 | BCKDHB | HTA11_99999970781_79442 | Human | Colorectum | MSS | 1.96e-02 | -2.91e-01 | 0.294 |
594 | BCKDHB | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.71e-02 | -3.57e-01 | 0.3859 |
594 | BCKDHB | HTA11_99999974143_84620 | Human | Colorectum | MSS | 1.74e-11 | -4.84e-01 | 0.3005 |
594 | BCKDHB | A001-C-207 | Human | Colorectum | FAP | 6.61e-04 | -2.70e-01 | 0.1278 |
594 | BCKDHB | A015-C-203 | Human | Colorectum | FAP | 6.07e-36 | -5.87e-01 | -0.1294 |
594 | BCKDHB | A015-C-204 | Human | Colorectum | FAP | 1.92e-07 | -3.67e-01 | -0.0228 |
594 | BCKDHB | A014-C-040 | Human | Colorectum | FAP | 2.57e-05 | -4.30e-01 | -0.1184 |
594 | BCKDHB | A002-C-201 | Human | Colorectum | FAP | 2.58e-16 | -3.94e-01 | 0.0324 |
594 | BCKDHB | A002-C-203 | Human | Colorectum | FAP | 8.94e-04 | -1.69e-01 | 0.2786 |
594 | BCKDHB | A001-C-119 | Human | Colorectum | FAP | 9.15e-14 | -6.21e-01 | -0.1557 |
594 | BCKDHB | A001-C-108 | Human | Colorectum | FAP | 1.70e-24 | -5.73e-01 | -0.0272 |
594 | BCKDHB | A002-C-205 | Human | Colorectum | FAP | 4.88e-31 | -6.50e-01 | -0.1236 |
594 | BCKDHB | A001-C-104 | Human | Colorectum | FAP | 2.51e-08 | -3.83e-01 | 0.0184 |
594 | BCKDHB | A015-C-005 | Human | Colorectum | FAP | 4.14e-07 | -3.81e-01 | -0.0336 |
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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:00442827 | Esophagus | ESCC | small molecule catabolic process | 201/8552 | 376/18723 | 1.35e-03 | 6.41e-03 | 201 |
GO:00090836 | Esophagus | ESCC | branched-chain amino acid catabolic process | 12/8552 | 15/18723 | 7.31e-03 | 2.63e-02 | 12 |
GO:00090815 | Esophagus | ESCC | branched-chain amino acid metabolic process | 14/8552 | 19/18723 | 1.27e-02 | 4.21e-02 | 14 |
GO:00463953 | Liver | NAFLD | carboxylic acid catabolic process | 73/1882 | 236/18723 | 4.16e-19 | 1.22e-15 | 73 |
GO:00160544 | Liver | NAFLD | organic acid catabolic process | 73/1882 | 240/18723 | 1.20e-18 | 2.34e-15 | 73 |
GO:00442825 | Liver | NAFLD | small molecule catabolic process | 91/1882 | 376/18723 | 8.96e-16 | 1.31e-12 | 91 |
GO:0009063 | Liver | NAFLD | cellular amino acid catabolic process | 36/1882 | 110/18723 | 6.56e-11 | 1.99e-08 | 36 |
GO:00065203 | Liver | NAFLD | cellular amino acid metabolic process | 63/1882 | 284/18723 | 1.14e-09 | 2.17e-07 | 63 |
GO:00316677 | Liver | NAFLD | response to nutrient levels | 85/1882 | 474/18723 | 8.23e-08 | 7.09e-06 | 85 |
GO:00075844 | Liver | NAFLD | response to nutrient | 36/1882 | 174/18723 | 2.06e-05 | 5.78e-04 | 36 |
GO:00090813 | Liver | NAFLD | branched-chain amino acid metabolic process | 8/1882 | 19/18723 | 2.81e-04 | 4.51e-03 | 8 |
GO:00090834 | Liver | NAFLD | branched-chain amino acid catabolic process | 7/1882 | 15/18723 | 3.18e-04 | 4.95e-03 | 7 |
GO:004428211 | Liver | Cirrhotic | small molecule catabolic process | 151/4634 | 376/18723 | 2.20e-11 | 1.34e-09 | 151 |
GO:001605411 | Liver | Cirrhotic | organic acid catabolic process | 104/4634 | 240/18723 | 1.91e-10 | 9.53e-09 | 104 |
GO:004639511 | Liver | Cirrhotic | carboxylic acid catabolic process | 102/4634 | 236/18723 | 3.41e-10 | 1.63e-08 | 102 |
GO:003166712 | Liver | Cirrhotic | response to nutrient levels | 174/4634 | 474/18723 | 3.08e-09 | 1.27e-07 | 174 |
GO:00090631 | Liver | Cirrhotic | cellular amino acid catabolic process | 49/4634 | 110/18723 | 4.47e-06 | 7.42e-05 | 49 |
GO:000652011 | Liver | Cirrhotic | cellular amino acid metabolic process | 103/4634 | 284/18723 | 8.88e-06 | 1.30e-04 | 103 |
GO:000908111 | Liver | Cirrhotic | branched-chain amino acid metabolic process | 14/4634 | 19/18723 | 1.00e-05 | 1.45e-04 | 14 |
GO:000758411 | Liver | Cirrhotic | response to nutrient | 67/4634 | 174/18723 | 3.83e-05 | 4.59e-04 | 67 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa00280 | Colorectum | AD | Valine, leucine and isoleucine degradation | 25/2092 | 48/8465 | 3.97e-05 | 3.41e-04 | 2.18e-04 | 25 |
hsa00640 | Colorectum | AD | Propanoate metabolism | 18/2092 | 32/8465 | 1.33e-04 | 1.11e-03 | 7.08e-04 | 18 |
hsa002801 | Colorectum | AD | Valine, leucine and isoleucine degradation | 25/2092 | 48/8465 | 3.97e-05 | 3.41e-04 | 2.18e-04 | 25 |
hsa006401 | Colorectum | AD | Propanoate metabolism | 18/2092 | 32/8465 | 1.33e-04 | 1.11e-03 | 7.08e-04 | 18 |
hsa002802 | Colorectum | MSS | Valine, leucine and isoleucine degradation | 21/1875 | 48/8465 | 6.73e-04 | 4.51e-03 | 2.76e-03 | 21 |
hsa006404 | Colorectum | MSS | Propanoate metabolism | 15/1875 | 32/8465 | 1.68e-03 | 9.05e-03 | 5.55e-03 | 15 |
hsa002803 | Colorectum | MSS | Valine, leucine and isoleucine degradation | 21/1875 | 48/8465 | 6.73e-04 | 4.51e-03 | 2.76e-03 | 21 |
hsa006405 | Colorectum | MSS | Propanoate metabolism | 15/1875 | 32/8465 | 1.68e-03 | 9.05e-03 | 5.55e-03 | 15 |
hsa006406 | Colorectum | FAP | Propanoate metabolism | 15/1404 | 32/8465 | 6.21e-05 | 6.10e-04 | 3.71e-04 | 15 |
hsa002804 | Colorectum | FAP | Valine, leucine and isoleucine degradation | 18/1404 | 48/8465 | 3.94e-04 | 3.06e-03 | 1.86e-03 | 18 |
hsa006407 | Colorectum | FAP | Propanoate metabolism | 15/1404 | 32/8465 | 6.21e-05 | 6.10e-04 | 3.71e-04 | 15 |
hsa002805 | Colorectum | FAP | Valine, leucine and isoleucine degradation | 18/1404 | 48/8465 | 3.94e-04 | 3.06e-03 | 1.86e-03 | 18 |
hsa006408 | Colorectum | CRC | Propanoate metabolism | 11/1091 | 32/8465 | 1.51e-03 | 1.17e-02 | 7.94e-03 | 11 |
hsa006409 | Colorectum | CRC | Propanoate metabolism | 11/1091 | 32/8465 | 1.51e-03 | 1.17e-02 | 7.94e-03 | 11 |
hsa002809 | Esophagus | ESCC | Valine, leucine and isoleucine degradation | 34/4205 | 48/8465 | 2.34e-03 | 6.54e-03 | 3.35e-03 | 34 |
hsa0028014 | Esophagus | ESCC | Valine, leucine and isoleucine degradation | 34/4205 | 48/8465 | 2.34e-03 | 6.54e-03 | 3.35e-03 | 34 |
hsa002806 | Liver | NAFLD | Valine, leucine and isoleucine degradation | 20/1043 | 48/8465 | 3.03e-07 | 1.65e-05 | 1.33e-05 | 20 |
hsa0064010 | Liver | NAFLD | Propanoate metabolism | 12/1043 | 32/8465 | 2.44e-04 | 4.45e-03 | 3.58e-03 | 12 |
hsa0028011 | Liver | NAFLD | Valine, leucine and isoleucine degradation | 20/1043 | 48/8465 | 3.03e-07 | 1.65e-05 | 1.33e-05 | 20 |
hsa0064011 | Liver | NAFLD | Propanoate metabolism | 12/1043 | 32/8465 | 2.44e-04 | 4.45e-03 | 3.58e-03 | 12 |
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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 |
BCKDHB | SNV | Missense_Mutation | c.289G>T | p.Asp97Tyr | p.D97Y | P21953 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
BCKDHB | insertion | Nonsense_Mutation | novel | c.1159_1160insCAAGCCCCTTCCTCATCTGCCCTGTAGGGCTGGGGAGGTGCT | p.Arg387delinsProSerProPheLeuIleCysProValGlyLeuGlyArgCysTer | p.R387delinsPSPFLICPVGLGRC* | P21953 | protein_coding | TCGA-AR-A0TY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | PD | ||
BCKDHB | SNV | Missense_Mutation | rs779150907 | c.971N>A | p.Arg324Gln | p.R324Q | P21953 | protein_coding | deleterious(0) | probably_damaging(0.991) | TCGA-AA-3812-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
BCKDHB | SNV | Missense_Mutation | rs755159101 | c.1160N>A | p.Arg387Gln | p.R387Q | P21953 | protein_coding | tolerated(0.09) | benign(0.012) | TCGA-AZ-6605-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | folfox | SD |
BCKDHB | SNV | Missense_Mutation | c.620G>A | p.Cys207Tyr | p.C207Y | P21953 | protein_coding | deleterious(0.01) | possibly_damaging(0.874) | TCGA-CK-5913-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
BCKDHB | SNV | Missense_Mutation | rs398124561 | c.1016N>T | p.Ser339Leu | p.S339L | P21953 | protein_coding | deleterious(0) | possibly_damaging(0.526) | TCGA-CM-4746-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
BCKDHB | SNV | Missense_Mutation | c.790N>A | p.Glu264Lys | p.E264K | P21953 | protein_coding | deleterious(0.01) | possibly_damaging(0.631) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD | |
BCKDHB | deletion | Frame_Shift_Del | novel | c.199delC | p.Gln67LysfsTer5 | p.Q67Kfs*5 | P21953 | protein_coding | TCGA-F4-6805-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR | ||
BCKDHB | SNV | Missense_Mutation | novel | c.427G>T | p.Ala143Ser | p.A143S | P21953 | protein_coding | deleterious(0.05) | benign(0.321) | TCGA-AJ-A2QO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
BCKDHB | SNV | Missense_Mutation | novel | c.518A>G | p.Asp173Gly | p.D173G | P21953 | protein_coding | tolerated(0.91) | benign(0.005) | 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 |
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