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Gene: NDUFS3 |
Gene summary for NDUFS3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NDUFS3 | Gene ID | 4722 |
Gene name | NADH:ubiquinone oxidoreductase core subunit S3 | |
Gene Alias | CI-30 | |
Cytomap | 11p11.2 | |
Gene Type | protein-coding | GO ID | GO:0001558 | UniProtAcc | O75489 |
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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 |
4722 | NDUFS3 | HTA11_3410_2000001011 | Human | Colorectum | AD | 9.20e-12 | 3.28e-01 | 0.0155 |
4722 | NDUFS3 | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.09e-14 | 5.60e-01 | -0.1808 |
4722 | NDUFS3 | HTA11_1938_2000001011 | Human | Colorectum | AD | 6.08e-12 | 6.49e-01 | -0.0811 |
4722 | NDUFS3 | HTA11_78_2000001011 | Human | Colorectum | AD | 3.23e-06 | 3.99e-01 | -0.1088 |
4722 | NDUFS3 | HTA11_347_2000001011 | Human | Colorectum | AD | 9.55e-33 | 7.29e-01 | -0.1954 |
4722 | NDUFS3 | HTA11_411_2000001011 | Human | Colorectum | SER | 1.99e-10 | 8.04e-01 | -0.2602 |
4722 | NDUFS3 | HTA11_2112_2000001011 | Human | Colorectum | SER | 1.25e-02 | 5.11e-01 | -0.2196 |
4722 | NDUFS3 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.26e-09 | 5.97e-01 | -0.1207 |
4722 | NDUFS3 | HTA11_83_2000001011 | Human | Colorectum | SER | 2.40e-11 | 6.78e-01 | -0.1526 |
4722 | NDUFS3 | HTA11_696_2000001011 | Human | Colorectum | AD | 2.65e-40 | 7.77e-01 | -0.1464 |
4722 | NDUFS3 | HTA11_866_2000001011 | Human | Colorectum | AD | 4.44e-12 | 3.78e-01 | -0.1001 |
4722 | NDUFS3 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.39e-26 | 8.41e-01 | -0.059 |
4722 | NDUFS3 | HTA11_2992_2000001011 | Human | Colorectum | SER | 3.71e-10 | 8.82e-01 | -0.1706 |
4722 | NDUFS3 | HTA11_5212_2000001011 | Human | Colorectum | AD | 4.00e-08 | 5.45e-01 | -0.2061 |
4722 | NDUFS3 | HTA11_5216_2000001011 | Human | Colorectum | SER | 3.56e-08 | 6.83e-01 | -0.1462 |
4722 | NDUFS3 | HTA11_546_2000001011 | Human | Colorectum | AD | 1.54e-12 | 6.30e-01 | -0.0842 |
4722 | NDUFS3 | HTA11_7862_2000001011 | Human | Colorectum | AD | 6.23e-06 | 3.93e-01 | -0.0179 |
4722 | NDUFS3 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.11e-19 | 5.70e-01 | 0.096 |
4722 | NDUFS3 | HTA11_4255_2000001011 | Human | Colorectum | SER | 1.19e-03 | 5.56e-01 | 0.0446 |
4722 | NDUFS3 | HTA11_8622_2000001021 | Human | Colorectum | SER | 6.34e-04 | 4.01e-01 | 0.0528 |
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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:0097193 | Colorectum | AD | intrinsic apoptotic signaling pathway | 108/3918 | 288/18723 | 6.25e-11 | 6.41e-09 | 108 |
GO:0006120 | Colorectum | AD | mitochondrial electron transport, NADH to ubiquinone | 32/3918 | 51/18723 | 1.12e-10 | 1.11e-08 | 32 |
GO:0010257 | Colorectum | AD | NADH dehydrogenase complex assembly | 34/3918 | 57/18723 | 2.15e-10 | 1.89e-08 | 34 |
GO:0032981 | Colorectum | AD | mitochondrial respiratory chain complex I assembly | 34/3918 | 57/18723 | 2.15e-10 | 1.89e-08 | 34 |
GO:0033108 | Colorectum | AD | mitochondrial respiratory chain complex assembly | 46/3918 | 93/18723 | 8.95e-10 | 6.91e-08 | 46 |
GO:2001242 | Colorectum | AD | regulation of intrinsic apoptotic signaling pathway | 67/3918 | 164/18723 | 4.94e-09 | 3.16e-07 | 67 |
GO:2001233 | Colorectum | AD | regulation of apoptotic signaling pathway | 119/3918 | 356/18723 | 2.14e-08 | 1.21e-06 | 119 |
GO:0016049 | Colorectum | AD | cell growth | 143/3918 | 482/18723 | 2.83e-06 | 8.09e-05 | 143 |
GO:0001558 | Colorectum | AD | regulation of cell growth | 124/3918 | 414/18723 | 7.67e-06 | 1.86e-04 | 124 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0471428 | Prostate | BPH | Thermogenesis | 110/1718 | 232/8465 | 5.16e-21 | 1.42e-19 | 8.78e-20 | 110 |
hsa0493226 | Prostate | BPH | Non-alcoholic fatty liver disease | 83/1718 | 155/8465 | 2.49e-20 | 6.32e-19 | 3.91e-19 | 83 |
hsa0502226 | Prostate | BPH | Pathways of neurodegeneration - multiple diseases | 180/1718 | 476/8465 | 7.70e-20 | 1.81e-18 | 1.12e-18 | 180 |
hsa0472325 | Prostate | BPH | Retrograde endocannabinoid signaling | 51/1718 | 148/8465 | 3.59e-05 | 2.57e-04 | 1.59e-04 | 51 |
hsa05012112 | Prostate | BPH | Parkinson disease | 143/1718 | 266/8465 | 1.19e-34 | 3.94e-32 | 2.44e-32 | 143 |
hsa05020111 | Prostate | BPH | Prion disease | 141/1718 | 273/8465 | 1.11e-31 | 1.23e-29 | 7.58e-30 | 141 |
hsa05016111 | Prostate | BPH | Huntington disease | 149/1718 | 306/8465 | 8.82e-30 | 7.27e-28 | 4.50e-28 | 149 |
hsa00190111 | Prostate | BPH | Oxidative phosphorylation | 83/1718 | 134/8465 | 3.75e-26 | 2.48e-24 | 1.53e-24 | 83 |
hsa05208113 | Prostate | BPH | Chemical carcinogenesis - reactive oxygen species | 114/1718 | 223/8465 | 3.05e-25 | 1.44e-23 | 8.91e-24 | 114 |
hsa05010111 | Prostate | BPH | Alzheimer disease | 165/1718 | 384/8465 | 4.03e-25 | 1.66e-23 | 1.03e-23 | 165 |
hsa05415112 | Prostate | BPH | Diabetic cardiomyopathy | 102/1718 | 203/8465 | 6.06e-22 | 2.00e-20 | 1.24e-20 | 102 |
hsa05014111 | Prostate | BPH | Amyotrophic lateral sclerosis | 151/1718 | 364/8465 | 3.37e-21 | 1.01e-19 | 6.25e-20 | 151 |
hsa04714112 | Prostate | BPH | Thermogenesis | 110/1718 | 232/8465 | 5.16e-21 | 1.42e-19 | 8.78e-20 | 110 |
hsa04932111 | Prostate | BPH | Non-alcoholic fatty liver disease | 83/1718 | 155/8465 | 2.49e-20 | 6.32e-19 | 3.91e-19 | 83 |
hsa05022111 | Prostate | BPH | Pathways of neurodegeneration - multiple diseases | 180/1718 | 476/8465 | 7.70e-20 | 1.81e-18 | 1.12e-18 | 180 |
hsa04723111 | Prostate | BPH | Retrograde endocannabinoid signaling | 51/1718 | 148/8465 | 3.59e-05 | 2.57e-04 | 1.59e-04 | 51 |
hsa0501229 | Prostate | Tumor | Parkinson disease | 144/1791 | 266/8465 | 3.33e-33 | 1.10e-30 | 6.83e-31 | 144 |
hsa0502027 | Prostate | Tumor | Prion disease | 142/1791 | 273/8465 | 2.80e-30 | 3.09e-28 | 1.92e-28 | 142 |
hsa0501627 | Prostate | Tumor | Huntington disease | 150/1791 | 306/8465 | 2.72e-28 | 2.25e-26 | 1.40e-26 | 150 |
hsa0019027 | Prostate | Tumor | Oxidative phosphorylation | 83/1791 | 134/8465 | 7.47e-25 | 4.12e-23 | 2.55e-23 | 83 |
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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 |
NDUFS3 | SNV | Missense_Mutation | c.700N>T | p.Asp234Tyr | p.D234Y | O75489 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-C8-A12Y-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
NDUFS3 | SNV | Missense_Mutation | novel | c.146N>G | p.Pro49Arg | p.P49R | O75489 | protein_coding | deleterious(0.02) | benign(0.319) | TCGA-C8-A8HR-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
NDUFS3 | insertion | Nonsense_Mutation | novel | c.307_308insTTCAAGCCCTTAAGTTCTTAGCTTGAGAACCTGGTAT | p.His103LeufsTer9 | p.H103Lfs*9 | O75489 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
NDUFS3 | SNV | Missense_Mutation | c.247N>A | p.Glu83Lys | p.E83K | O75489 | protein_coding | deleterious(0) | benign(0.194) | TCGA-IR-A3LI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
NDUFS3 | SNV | Missense_Mutation | rs201457989 | c.34N>T | p.Arg12Cys | p.R12C | O75489 | protein_coding | deleterious(0) | benign(0.306) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
NDUFS3 | SNV | Missense_Mutation | c.214N>C | p.Tyr72His | p.Y72H | O75489 | protein_coding | deleterious(0.03) | probably_damaging(0.962) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NDUFS3 | SNV | Missense_Mutation | novel | c.263T>A | p.Ile88Asn | p.I88N | O75489 | protein_coding | deleterious(0) | possibly_damaging(0.794) | TCGA-AA-3949-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
NDUFS3 | SNV | Missense_Mutation | c.11N>T | p.Ala4Val | p.A4V | O75489 | protein_coding | tolerated(0.07) | benign(0) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NDUFS3 | SNV | Missense_Mutation | rs747054142 | c.432G>C | p.Lys144Asn | p.K144N | O75489 | protein_coding | deleterious(0) | probably_damaging(0.966) | TCGA-CM-4746-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
NDUFS3 | SNV | Missense_Mutation | novel | c.127N>G | p.Thr43Ala | p.T43A | O75489 | protein_coding | tolerated(0.42) | benign(0.005) | TCGA-A5-A1OF-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 |
4722 | NDUFS3 | DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL3545135 | NV-128 | |
4722 | NDUFS3 | DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL3545320 | ME-344 | |
4722 | NDUFS3 | DRUGGABLE GENOME, ENZYME | inhibitor | CHEMBL1703 | METFORMIN HYDROCHLORIDE |
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