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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 | HTA11_3410_2000001011 | Human | Colorectum | AD | 5.90e-11 | 2.41e-01 | 0.0155 |
| 6392 | SDHD | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.14e-15 | 4.33e-01 | -0.1808 |
| 6392 | SDHD | HTA11_2951_2000001011 | Human | Colorectum | AD | 3.34e-04 | 2.80e-01 | 0.0216 |
| 6392 | SDHD | HTA11_1938_2000001011 | Human | Colorectum | AD | 8.04e-15 | 5.17e-01 | -0.0811 |
| 6392 | SDHD | HTA11_78_2000001011 | Human | Colorectum | AD | 6.88e-27 | 6.94e-01 | -0.1088 |
| 6392 | SDHD | HTA11_347_2000001011 | Human | Colorectum | AD | 1.41e-41 | 7.73e-01 | -0.1954 |
| 6392 | SDHD | HTA11_411_2000001011 | Human | Colorectum | SER | 1.35e-12 | 8.01e-01 | -0.2602 |
| 6392 | SDHD | HTA11_3361_2000001011 | Human | Colorectum | AD | 3.26e-09 | 3.70e-01 | -0.1207 |
| 6392 | SDHD | HTA11_83_2000001011 | Human | Colorectum | SER | 1.12e-08 | 3.22e-01 | -0.1526 |
| 6392 | SDHD | HTA11_696_2000001011 | Human | Colorectum | AD | 2.10e-17 | 3.37e-01 | -0.1464 |
| 6392 | SDHD | HTA11_866_2000001011 | Human | Colorectum | AD | 7.82e-13 | 2.67e-01 | -0.1001 |
| 6392 | SDHD | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.44e-15 | 3.55e-01 | -0.059 |
| 6392 | SDHD | HTA11_2992_2000001011 | Human | Colorectum | SER | 7.86e-21 | 7.82e-01 | -0.1706 |
| 6392 | SDHD | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.13e-20 | 7.47e-01 | -0.2061 |
| 6392 | SDHD | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.49e-08 | 4.90e-01 | -0.1462 |
| 6392 | SDHD | HTA11_546_2000001011 | Human | Colorectum | AD | 4.83e-05 | 2.45e-01 | -0.0842 |
| 6392 | SDHD | HTA11_7862_2000001011 | Human | Colorectum | AD | 5.05e-17 | 6.40e-01 | -0.0179 |
| 6392 | SDHD | HTA11_866_3004761011 | Human | Colorectum | AD | 5.18e-29 | 5.68e-01 | 0.096 |
| 6392 | SDHD | HTA11_4255_2000001011 | Human | Colorectum | SER | 1.84e-10 | 4.41e-01 | 0.0446 |
| 6392 | SDHD | HTA11_8622_2000001021 | Human | Colorectum | SER | 3.15e-09 | 4.03e-01 | 0.0528 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:004277512 | Liver | HCC | mitochondrial ATP synthesis coupled electron transport | 74/7958 | 95/18723 | 1.94e-12 | 9.18e-11 | 74 |
| GO:001964612 | Liver | HCC | aerobic electron transport chain | 67/7958 | 87/18723 | 5.43e-11 | 2.00e-09 | 67 |
| GO:000609911 | Liver | HCC | tricarboxylic acid cycle | 27/7958 | 30/18723 | 7.59e-08 | 1.52e-06 | 27 |
| GO:002290018 | Oral cavity | OSCC | electron transport chain | 126/7305 | 175/18723 | 6.65e-19 | 8.42e-17 | 126 |
| GO:000609118 | Oral cavity | OSCC | generation of precursor metabolites and energy | 286/7305 | 490/18723 | 1.45e-18 | 1.71e-16 | 286 |
| GO:000906018 | Oral cavity | OSCC | aerobic respiration | 133/7305 | 189/18723 | 1.79e-18 | 2.02e-16 | 133 |
| GO:004533318 | Oral cavity | OSCC | cellular respiration | 153/7305 | 230/18723 | 2.07e-17 | 1.87e-15 | 153 |
| GO:004277318 | Oral cavity | OSCC | ATP synthesis coupled electron transport | 75/7305 | 95/18723 | 1.95e-15 | 1.33e-13 | 75 |
| GO:004277518 | Oral cavity | OSCC | mitochondrial ATP synthesis coupled electron transport | 75/7305 | 95/18723 | 1.95e-15 | 1.33e-13 | 75 |
| GO:002290418 | Oral cavity | OSCC | respiratory electron transport chain | 86/7305 | 114/18723 | 2.43e-15 | 1.63e-13 | 86 |
| GO:001598018 | Oral cavity | OSCC | energy derivation by oxidation of organic compounds | 190/7305 | 318/18723 | 4.10e-14 | 2.26e-12 | 190 |
| GO:001964618 | Oral cavity | OSCC | aerobic electron transport chain | 68/7305 | 87/18723 | 9.88e-14 | 5.17e-12 | 68 |
| GO:004603420 | Oral cavity | OSCC | ATP metabolic process | 166/7305 | 277/18723 | 1.16e-12 | 5.12e-11 | 166 |
| GO:000611919 | Oral cavity | OSCC | oxidative phosphorylation | 96/7305 | 141/18723 | 2.33e-12 | 9.75e-11 | 96 |
| GO:00060996 | Oral cavity | OSCC | tricarboxylic acid cycle | 26/7305 | 30/18723 | 9.63e-08 | 1.66e-06 | 26 |
| GO:002290019 | Oral cavity | LP | electron transport chain | 108/4623 | 175/18723 | 2.21e-25 | 9.90e-23 | 108 |
| GO:000906019 | Oral cavity | LP | aerobic respiration | 111/4623 | 189/18723 | 1.68e-23 | 5.85e-21 | 111 |
| GO:004277319 | Oral cavity | LP | ATP synthesis coupled electron transport | 69/4623 | 95/18723 | 9.69e-23 | 3.04e-20 | 69 |
| GO:004277519 | Oral cavity | LP | mitochondrial ATP synthesis coupled electron transport | 69/4623 | 95/18723 | 9.69e-23 | 3.04e-20 | 69 |
| GO:004533319 | Oral cavity | LP | cellular respiration | 124/4623 | 230/18723 | 1.35e-21 | 3.38e-19 | 124 |
| Page: 1 2 3 4 5 6 7 8 |
| 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 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| Page: 1 2 |
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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 |
| Page: 1 |
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