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Gene: NOTCH3 |
Gene summary for NOTCH3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | NOTCH3 | Gene ID | 4854 |
Gene name | notch receptor 3 | |
Gene Alias | CADASIL | |
Cytomap | 19p13.12 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q9UM47 |
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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 |
4854 | NOTCH3 | CCI_1 | Human | Cervix | CC | 4.42e-13 | 7.18e-01 | 0.528 |
4854 | NOTCH3 | CCI_3 | Human | Cervix | CC | 6.08e-06 | 5.85e-01 | 0.516 |
4854 | NOTCH3 | Tumor | Human | Cervix | CC | 1.56e-20 | 4.26e-01 | 0.1241 |
4854 | NOTCH3 | sample3 | Human | Cervix | CC | 4.03e-21 | 4.11e-01 | 0.1387 |
4854 | NOTCH3 | T1 | Human | Cervix | CC | 8.72e-08 | 2.99e-01 | 0.0918 |
4854 | NOTCH3 | T3 | Human | Cervix | CC | 8.69e-23 | 3.87e-01 | 0.1389 |
4854 | NOTCH3 | LZE7T | Human | Esophagus | ESCC | 2.03e-03 | 2.59e-01 | 0.0667 |
4854 | NOTCH3 | LZE20T | Human | Esophagus | ESCC | 4.83e-02 | 1.17e-01 | 0.0662 |
4854 | NOTCH3 | LZE21T | Human | Esophagus | ESCC | 1.38e-07 | 4.50e-01 | 0.0655 |
4854 | NOTCH3 | LZE6T | Human | Esophagus | ESCC | 2.81e-02 | 1.45e-01 | 0.0845 |
4854 | NOTCH3 | P1T-E | Human | Esophagus | ESCC | 1.69e-06 | 6.38e-01 | 0.0875 |
4854 | NOTCH3 | P4T-E | Human | Esophagus | ESCC | 1.85e-05 | 2.81e-01 | 0.1323 |
4854 | NOTCH3 | P5T-E | Human | Esophagus | ESCC | 7.89e-11 | 2.64e-01 | 0.1327 |
4854 | NOTCH3 | P8T-E | Human | Esophagus | ESCC | 3.90e-26 | 6.72e-01 | 0.0889 |
4854 | NOTCH3 | P9T-E | Human | Esophagus | ESCC | 3.61e-16 | 5.39e-01 | 0.1131 |
4854 | NOTCH3 | P12T-E | Human | Esophagus | ESCC | 8.03e-09 | 2.61e-01 | 0.1122 |
4854 | NOTCH3 | P15T-E | Human | Esophagus | ESCC | 8.63e-10 | 3.12e-01 | 0.1149 |
4854 | NOTCH3 | P17T-E | Human | Esophagus | ESCC | 1.38e-06 | 4.11e-01 | 0.1278 |
4854 | NOTCH3 | P22T-E | Human | Esophagus | ESCC | 5.58e-11 | 2.47e-01 | 0.1236 |
4854 | NOTCH3 | P23T-E | Human | Esophagus | ESCC | 1.44e-12 | 4.50e-01 | 0.108 |
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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:00615647 | Cervix | CC | axon development | 89/2311 | 467/18723 | 1.71e-05 | 3.27e-04 | 89 |
GO:00072194 | Cervix | CC | Notch signaling pathway | 39/2311 | 172/18723 | 1.08e-04 | 1.38e-03 | 39 |
GO:00074097 | Cervix | CC | axonogenesis | 78/2311 | 418/18723 | 1.14e-04 | 1.43e-03 | 78 |
GO:00072197 | Esophagus | ESCC | Notch signaling pathway | 106/8552 | 172/18723 | 1.74e-05 | 1.55e-04 | 106 |
GO:006156415 | Esophagus | ESCC | axon development | 251/8552 | 467/18723 | 2.41e-04 | 1.49e-03 | 251 |
GO:000740915 | Esophagus | ESCC | axonogenesis | 219/8552 | 418/18723 | 3.14e-03 | 1.31e-02 | 219 |
GO:00072196 | Oral cavity | OSCC | Notch signaling pathway | 92/7305 | 172/18723 | 7.84e-05 | 6.08e-04 | 92 |
GO:006156410 | Oral cavity | OSCC | axon development | 207/7305 | 467/18723 | 1.01e-02 | 3.51e-02 | 207 |
GO:006156421 | Oral cavity | NEOLP | axon development | 78/2005 | 467/18723 | 4.49e-05 | 6.26e-04 | 78 |
GO:000740914 | Oral cavity | NEOLP | axonogenesis | 71/2005 | 418/18723 | 5.64e-05 | 7.62e-04 | 71 |
GO:000721921 | Oral cavity | NEOLP | Notch signaling pathway | 32/2005 | 172/18723 | 1.31e-03 | 9.48e-03 | 32 |
GO:006156419 | Thyroid | PTC | axon development | 199/5968 | 467/18723 | 5.27e-07 | 8.53e-06 | 199 |
GO:000740918 | Thyroid | PTC | axonogenesis | 178/5968 | 418/18723 | 2.17e-06 | 2.91e-05 | 178 |
GO:00072199 | Thyroid | PTC | Notch signaling pathway | 70/5968 | 172/18723 | 8.82e-03 | 3.67e-02 | 70 |
GO:006156423 | Thyroid | ATC | axon development | 220/6293 | 467/18723 | 6.85e-10 | 1.80e-08 | 220 |
GO:000740919 | Thyroid | ATC | axonogenesis | 197/6293 | 418/18723 | 5.09e-09 | 1.13e-07 | 197 |
GO:000721915 | Thyroid | ATC | Notch signaling pathway | 79/6293 | 172/18723 | 5.08e-04 | 2.96e-03 | 79 |
GO:00074113 | Thyroid | ATC | axon guidance | 96/6293 | 227/18723 | 3.74e-03 | 1.63e-02 | 96 |
GO:00974853 | Thyroid | ATC | neuron projection guidance | 96/6293 | 228/18723 | 4.36e-03 | 1.81e-02 | 96 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa051657 | Cervix | CC | Human papillomavirus infection | 74/1267 | 331/8465 | 1.70e-04 | 1.02e-03 | 6.03e-04 | 74 |
hsa0491918 | Cervix | CC | Thyroid hormone signaling pathway | 33/1267 | 121/8465 | 3.11e-04 | 1.65e-03 | 9.78e-04 | 33 |
hsa015223 | Cervix | CC | Endocrine resistance | 28/1267 | 98/8465 | 3.82e-04 | 1.87e-03 | 1.11e-03 | 28 |
hsa04330 | Cervix | CC | Notch signaling pathway | 17/1267 | 62/8465 | 7.99e-03 | 2.56e-02 | 1.51e-02 | 17 |
hsa05224 | Cervix | CC | Breast cancer | 32/1267 | 147/8465 | 1.66e-02 | 4.88e-02 | 2.88e-02 | 32 |
hsa0516512 | Cervix | CC | Human papillomavirus infection | 74/1267 | 331/8465 | 1.70e-04 | 1.02e-03 | 6.03e-04 | 74 |
hsa0491919 | Cervix | CC | Thyroid hormone signaling pathway | 33/1267 | 121/8465 | 3.11e-04 | 1.65e-03 | 9.78e-04 | 33 |
hsa0152212 | Cervix | CC | Endocrine resistance | 28/1267 | 98/8465 | 3.82e-04 | 1.87e-03 | 1.11e-03 | 28 |
hsa043301 | Cervix | CC | Notch signaling pathway | 17/1267 | 62/8465 | 7.99e-03 | 2.56e-02 | 1.51e-02 | 17 |
hsa052241 | Cervix | CC | Breast cancer | 32/1267 | 147/8465 | 1.66e-02 | 4.88e-02 | 2.88e-02 | 32 |
hsa0516510 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa0491928 | Esophagus | ESCC | Thyroid hormone signaling pathway | 78/4205 | 121/8465 | 6.79e-04 | 2.23e-03 | 1.14e-03 | 78 |
hsa015227 | Esophagus | ESCC | Endocrine resistance | 63/4205 | 98/8465 | 2.38e-03 | 6.58e-03 | 3.37e-03 | 63 |
hsa043306 | Esophagus | ESCC | Notch signaling pathway | 42/4205 | 62/8465 | 2.97e-03 | 7.97e-03 | 4.08e-03 | 42 |
hsa046585 | Esophagus | ESCC | Th1 and Th2 cell differentiation | 58/4205 | 92/8465 | 6.49e-03 | 1.60e-02 | 8.19e-03 | 58 |
hsa0516515 | Esophagus | ESCC | Human papillomavirus infection | 215/4205 | 331/8465 | 7.86e-09 | 7.12e-08 | 3.65e-08 | 215 |
hsa04919113 | Esophagus | ESCC | Thyroid hormone signaling pathway | 78/4205 | 121/8465 | 6.79e-04 | 2.23e-03 | 1.14e-03 | 78 |
hsa0152215 | Esophagus | ESCC | Endocrine resistance | 63/4205 | 98/8465 | 2.38e-03 | 6.58e-03 | 3.37e-03 | 63 |
hsa0433013 | Esophagus | ESCC | Notch signaling pathway | 42/4205 | 62/8465 | 2.97e-03 | 7.97e-03 | 4.08e-03 | 42 |
hsa0465812 | Esophagus | ESCC | Th1 and Th2 cell differentiation | 58/4205 | 92/8465 | 6.49e-03 | 1.60e-02 | 8.19e-03 | 58 |
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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 |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | Breast | DCIS |
DLK1 | NOTCH3 | DLK1_NOTCH3 | NOTCH | Breast | Healthy |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | Breast | Healthy |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | Breast | IDC |
DLL4 | NOTCH3 | DLL4_NOTCH3 | NOTCH | Cervix | ADJ |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | Cervix | CC |
JAG2 | NOTCH3 | JAG2_NOTCH3 | NOTCH | Cervix | CC |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | Cervix | Precancer |
DLL1 | NOTCH3 | DLL1_NOTCH3 | NOTCH | CRC | CRC |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | CRC | CRC |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | CRC | FAP |
DLL4 | NOTCH3 | DLL4_NOTCH3 | NOTCH | CRC | MSI-H |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | CRC | MSI-H |
JAG2 | NOTCH3 | JAG2_NOTCH3 | NOTCH | CRC | MSI-H |
DLL1 | NOTCH3 | DLL1_NOTCH3 | NOTCH | CRC | MSS |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | CRC | MSS |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | Endometrium | ADJ |
DLL4 | NOTCH3 | DLL4_NOTCH3 | NOTCH | Endometrium | AEH |
JAG1 | NOTCH3 | JAG1_NOTCH3 | NOTCH | Endometrium | AEH |
DLL4 | NOTCH3 | DLL4_NOTCH3 | NOTCH | Endometrium | EEC |
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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 |
NOTCH3 | SNV | Missense_Mutation | c.4879N>T | p.Arg1627Trp | p.R1627W | Q9UM47 | protein_coding | tolerated(0.17) | probably_damaging(0.965) | TCGA-EI-6510-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
NOTCH3 | SNV | Missense_Mutation | novel | c.6802N>A | p.Glu2268Lys | p.E2268K | Q9UM47 | protein_coding | deleterious(0.03) | benign(0.06) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
NOTCH3 | SNV | Missense_Mutation | novel | c.3649N>A | p.Ala1217Thr | p.A1217T | Q9UM47 | protein_coding | tolerated(0.48) | benign(0.017) | TCGA-EI-6917-01 | Colorectum | rectum adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5fluorouracil+oxaciplatina+l-folinian | SD |
NOTCH3 | SNV | Missense_Mutation | novel | c.6511G>A | p.Asp2171Asn | p.D2171N | Q9UM47 | protein_coding | tolerated(0.2) | possibly_damaging(0.648) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
NOTCH3 | SNV | Missense_Mutation | novel | c.1411G>T | p.Asp471Tyr | p.D471Y | Q9UM47 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
NOTCH3 | deletion | Frame_Shift_Del | c.125delC | p.Pro42LeufsTer194 | p.P42Lfs*194 | Q9UM47 | protein_coding | TCGA-AD-5900-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |||
NOTCH3 | insertion | Frame_Shift_Ins | rs749829137 | c.125_126insC | p.Cys43LeufsTer32 | p.C43Lfs*32 | Q9UM47 | protein_coding | TCGA-G4-6628-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | ||
NOTCH3 | SNV | Missense_Mutation | novel | c.5375C>T | p.Pro1792Leu | p.P1792L | Q9UM47 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NOTCH3 | SNV | Missense_Mutation | novel | c.3415G>A | p.Asp1139Asn | p.D1139N | Q9UM47 | protein_coding | tolerated(0.14) | possibly_damaging(0.889) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NOTCH3 | SNV | Missense_Mutation | novel | c.1971G>T | p.Glu657Asp | p.E657D | Q9UM47 | protein_coding | tolerated(0.62) | benign(0.003) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | 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 |
4854 | NOTCH3 | CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | TAREXTUMAB | TAREXTUMAB | 25934888,24525742 | |
4854 | NOTCH3 | CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | inhibitor | RO4929097 | RG-4733 | |
4854 | NOTCH3 | CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | antibody | REGN421 | ||
4854 | NOTCH3 | CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | inhibitor | PF-03084014 | NIROGACESTAT | |
4854 | NOTCH3 | CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | Tarextumab | TAREXTUMAB | ||
4854 | NOTCH3 | CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | antibody | 252166663 | TAREXTUMAB | |
4854 | NOTCH3 | CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | inhibitor | MK0752 | ||
4854 | NOTCH3 | CELL SURFACE, CLINICALLY ACTIONABLE, DRUGGABLE GENOME | OMP-59R5 | TAREXTUMAB |
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