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Gene: SDHD |
Gene summary for SDHD |
Gene summary. |
Gene information | Species | Human | Gene symbol | SDHD | Gene ID | 6392 |
Gene name | succinate dehydrogenase complex subunit D | |
Gene Alias | CBT1 | |
Cytomap | 11q23.1 | |
Gene Type | protein-coding | GO ID | GO:0006091 | UniProtAcc | A0A0S2Z4H7 |
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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 |
6392 | SDHD | C09 | Human | Oral cavity | OSCC | 3.80e-16 | 6.30e-01 | 0.1431 |
6392 | SDHD | LN22 | Human | Oral cavity | OSCC | 2.50e-12 | 1.53e+00 | 0.1733 |
6392 | SDHD | LN38 | Human | Oral cavity | OSCC | 4.23e-04 | 1.21e+00 | 0.168 |
6392 | SDHD | LN46 | Human | Oral cavity | OSCC | 9.97e-03 | 5.09e-01 | 0.1666 |
6392 | SDHD | LP15 | Human | Oral cavity | LP | 1.56e-14 | 2.12e+00 | 0.2174 |
6392 | SDHD | LP17 | Human | Oral cavity | LP | 1.17e-10 | 1.92e+00 | 0.2349 |
6392 | SDHD | SYSMH1 | Human | Oral cavity | OSCC | 2.90e-26 | 6.56e-01 | 0.1127 |
6392 | SDHD | SYSMH2 | Human | Oral cavity | OSCC | 1.43e-37 | 1.38e+00 | 0.2326 |
6392 | SDHD | SYSMH3 | Human | Oral cavity | OSCC | 1.10e-25 | 9.89e-01 | 0.2442 |
6392 | SDHD | SYSMH4 | Human | Oral cavity | OSCC | 1.06e-13 | 2.93e-01 | 0.1226 |
6392 | SDHD | SYSMH6 | Human | Oral cavity | OSCC | 2.70e-22 | 7.23e-01 | 0.1275 |
6392 | SDHD | P4_S8_cSCC | Human | Skin | cSCC | 5.20e-04 | -2.95e-02 | -0.3095 |
6392 | SDHD | P5_S10_cSCC | Human | Skin | cSCC | 1.26e-04 | -1.72e-01 | -0.299 |
6392 | SDHD | P1_cSCC | Human | Skin | cSCC | 9.66e-34 | 1.14e+00 | 0.0292 |
6392 | SDHD | P2_cSCC | Human | Skin | cSCC | 1.38e-17 | 5.93e-01 | -0.024 |
6392 | SDHD | P4_cSCC | Human | Skin | cSCC | 5.62e-20 | 6.38e-01 | -0.00290000000000005 |
6392 | SDHD | P10_cSCC | Human | Skin | cSCC | 2.93e-23 | 7.99e-01 | 0.1017 |
6392 | SDHD | cSCC_p7 | Human | Skin | cSCC | 4.08e-02 | -3.59e-01 | -0.2332 |
6392 | SDHD | cSCC_p8 | Human | Skin | cSCC | 3.21e-03 | -7.42e-02 | -0.1971 |
6392 | SDHD | cSCC_p9 | Human | Skin | cSCC | 1.50e-04 | -1.64e-01 | -0.1991 |
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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:0046034 | Colorectum | AD | ATP metabolic process | 142/3918 | 277/18723 | 2.64e-29 | 8.26e-26 | 142 |
GO:0006091 | Colorectum | AD | generation of precursor metabolites and energy | 209/3918 | 490/18723 | 3.17e-28 | 6.61e-25 | 209 |
GO:0009060 | Colorectum | AD | aerobic respiration | 108/3918 | 189/18723 | 9.14e-28 | 1.43e-24 | 108 |
GO:0045333 | Colorectum | AD | cellular respiration | 119/3918 | 230/18723 | 3.21e-25 | 4.02e-22 | 119 |
GO:0006119 | Colorectum | AD | oxidative phosphorylation | 83/3918 | 141/18723 | 7.95e-23 | 8.30e-20 | 83 |
GO:0015980 | Colorectum | AD | energy derivation by oxidation of organic compounds | 143/3918 | 318/18723 | 2.78e-22 | 2.49e-19 | 143 |
GO:0022900 | Colorectum | AD | electron transport chain | 89/3918 | 175/18723 | 1.42e-18 | 8.91e-16 | 89 |
GO:0019646 | Colorectum | AD | aerobic electron transport chain | 53/3918 | 87/18723 | 5.58e-16 | 2.16e-13 | 53 |
GO:0042773 | Colorectum | AD | ATP synthesis coupled electron transport | 56/3918 | 95/18723 | 6.76e-16 | 2.22e-13 | 56 |
GO:0042775 | Colorectum | AD | mitochondrial ATP synthesis coupled electron transport | 56/3918 | 95/18723 | 6.76e-16 | 2.22e-13 | 56 |
GO:0022904 | Colorectum | AD | respiratory electron transport chain | 63/3918 | 114/18723 | 8.23e-16 | 2.45e-13 | 63 |
GO:0006099 | Colorectum | AD | tricarboxylic acid cycle | 19/3918 | 30/18723 | 5.82e-07 | 2.09e-05 | 19 |
GO:00090601 | Colorectum | SER | aerobic respiration | 96/2897 | 189/18723 | 5.53e-30 | 1.70e-26 | 96 |
GO:00460341 | Colorectum | SER | ATP metabolic process | 117/2897 | 277/18723 | 5.54e-27 | 1.13e-23 | 117 |
GO:00453331 | Colorectum | SER | cellular respiration | 103/2897 | 230/18723 | 2.35e-26 | 3.61e-23 | 103 |
GO:00060911 | Colorectum | SER | generation of precursor metabolites and energy | 168/2897 | 490/18723 | 1.39e-25 | 1.70e-22 | 168 |
GO:00061191 | Colorectum | SER | oxidative phosphorylation | 75/2897 | 141/18723 | 2.35e-25 | 2.40e-22 | 75 |
GO:00159801 | Colorectum | SER | energy derivation by oxidation of organic compounds | 119/2897 | 318/18723 | 5.28e-22 | 4.62e-19 | 119 |
GO:00229001 | Colorectum | SER | electron transport chain | 77/2897 | 175/18723 | 1.77e-19 | 1.36e-16 | 77 |
GO:00427731 | Colorectum | SER | ATP synthesis coupled electron transport | 51/2897 | 95/18723 | 6.48e-18 | 3.98e-15 | 51 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05012 | Colorectum | AD | Parkinson disease | 147/2092 | 266/8465 | 2.53e-27 | 8.48e-25 | 5.41e-25 | 147 |
hsa05208 | Colorectum | AD | Chemical carcinogenesis - reactive oxygen species | 126/2092 | 223/8465 | 1.01e-24 | 1.68e-22 | 1.07e-22 | 126 |
hsa00190 | Colorectum | AD | Oxidative phosphorylation | 86/2092 | 134/8465 | 2.47e-22 | 2.76e-20 | 1.76e-20 | 86 |
hsa05415 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
hsa05010 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
hsa05016 | Colorectum | AD | Huntington disease | 147/2092 | 306/8465 | 1.93e-19 | 9.26e-18 | 5.91e-18 | 147 |
hsa04714 | Colorectum | AD | Thermogenesis | 120/2092 | 232/8465 | 2.76e-19 | 1.16e-17 | 7.37e-18 | 120 |
hsa04932 | Colorectum | AD | Non-alcoholic fatty liver disease | 90/2092 | 155/8465 | 4.83e-19 | 1.80e-17 | 1.15e-17 | 90 |
hsa05020 | Colorectum | AD | Prion disease | 133/2092 | 273/8465 | 2.47e-18 | 8.29e-17 | 5.29e-17 | 133 |
hsa05014 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
hsa05022 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
hsa01200 | Colorectum | AD | Carbon metabolism | 55/2092 | 115/8465 | 5.53e-08 | 8.42e-07 | 5.37e-07 | 55 |
hsa00020 | Colorectum | AD | Citrate cycle (TCA cycle) | 20/2092 | 30/8465 | 1.43e-06 | 1.77e-05 | 1.13e-05 | 20 |
hsa050121 | Colorectum | AD | Parkinson disease | 147/2092 | 266/8465 | 2.53e-27 | 8.48e-25 | 5.41e-25 | 147 |
hsa052081 | Colorectum | AD | Chemical carcinogenesis - reactive oxygen species | 126/2092 | 223/8465 | 1.01e-24 | 1.68e-22 | 1.07e-22 | 126 |
hsa001901 | Colorectum | AD | Oxidative phosphorylation | 86/2092 | 134/8465 | 2.47e-22 | 2.76e-20 | 1.76e-20 | 86 |
hsa054151 | Colorectum | AD | Diabetic cardiomyopathy | 114/2092 | 203/8465 | 3.65e-22 | 3.06e-20 | 1.95e-20 | 114 |
hsa050101 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
hsa050161 | Colorectum | AD | Huntington disease | 147/2092 | 306/8465 | 1.93e-19 | 9.26e-18 | 5.91e-18 | 147 |
hsa047141 | Colorectum | AD | Thermogenesis | 120/2092 | 232/8465 | 2.76e-19 | 1.16e-17 | 7.37e-18 | 120 |
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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 |
SDHD | SNV | Missense_Mutation | c.350N>T | p.Gly117Val | p.G117V | O14521 | protein_coding | deleterious(0.04) | possibly_damaging(0.446) | TCGA-AA-A010-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Chemotherapy | folinic | CR | |
SDHD | SNV | Missense_Mutation | c.10N>T | p.Leu4Phe | p.L4F | O14521 | protein_coding | tolerated(0.06) | possibly_damaging(0.499) | TCGA-AZ-6599-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SDHD | SNV | Missense_Mutation | c.200N>T | p.Thr67Ile | p.T67I | O14521 | protein_coding | deleterious(0.01) | possibly_damaging(0.888) | TCGA-CK-6746-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SDHD | SNV | Missense_Mutation | c.65G>A | p.Arg22Gln | p.R22Q | O14521 | protein_coding | tolerated(0.63) | benign(0) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
SDHD | SNV | Missense_Mutation | c.134N>T | p.Gly45Val | p.G45V | O14521 | protein_coding | tolerated(0.15) | benign(0.074) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
SDHD | SNV | Missense_Mutation | rs758784300 | c.356N>T | p.Ala119Val | p.A119V | O14521 | protein_coding | tolerated(0.17) | benign(0.005) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
SDHD | SNV | Missense_Mutation | c.65N>A | p.Arg22Gln | p.R22Q | O14521 | protein_coding | tolerated(0.63) | benign(0) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SDHD | SNV | Missense_Mutation | c.466N>A | p.Leu156Met | p.L156M | O14521 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SDHD | SNV | Missense_Mutation | rs202198133 | c.205N>A | p.Glu69Lys | p.E69K | O14521 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-BS-A0UV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
SDHD | SNV | Missense_Mutation | c.65N>A | p.Arg22Gln | p.R22Q | O14521 | protein_coding | tolerated(0.63) | benign(0) | TCGA-EO-A3AV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | 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 |
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