Tissue | Expression Dynamics | Abbreviation |
Cervix | ![The image shows the 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.](images/deg_images/Cervix/NF1_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
Colorectum (GSE201348) | ![The image shows the 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.](images/deg_images/Colorectum/Becker/NF1_pca_on_diff_genes.png) | FAP: Familial adenomatous polyposis |
CRC: Colorectal cancer |
Colorectum (HTA11) | ![The image shows the 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.](images/deg_images/Colorectum/Chen/NF1_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
Endometrium | ![The image shows the 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.](images/deg_images/Endometrium/NF1_pca_on_diff_genes.png) | AEH: Atypical endometrial hyperplasia |
EEC: Endometrioid Cancer |
Esophagus | ![The image shows the 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.](images/deg_images/Esophagus/NF1_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
Liver | ![The image shows the 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.](images/deg_images/Liver/NF1_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
Lung | ![The image shows the 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.](images/deg_images/Lung/NF1_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
Oral Cavity | ![The image shows the 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.](images/deg_images/OralCavity/NF1_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
Prostate | ![The image shows the 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.](images/deg_images/Prostate/NF1_pca_on_diff_genes.png) | BPH: Benign Prostatic Hyperplasia |
Skin | ![The image shows the 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.](images/deg_images/Skin/NF1_pca_on_diff_genes.png) | AK: Actinic keratosis |
cSCC: Cutaneous squamous cell carcinoma |
SCCIS:squamous cell carcinoma in situ |
Thyroid | ![The image shows the 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.](images/deg_images/Thyroid/NF1_pca_on_diff_genes.png) | ATC: Anaplastic thyroid cancer |
HT: Hashimoto's thyroiditis |
PTC: Papillary thyroid cancer |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:004205916 | Thyroid | ATC | negative regulation of epidermal growth factor receptor signaling pathway | 21/6293 | 28/18723 | 8.94e-06 | 8.95e-05 | 21 |
GO:0010038210 | Thyroid | ATC | response to metal ion | 165/6293 | 373/18723 | 1.07e-05 | 1.05e-04 | 165 |
GO:190118515 | Thyroid | ATC | negative regulation of ERBB signaling pathway | 23/6293 | 32/18723 | 1.09e-05 | 1.07e-04 | 23 |
GO:003424412 | Thyroid | ATC | negative regulation of transcription elongation from RNA polymerase II promoter | 14/6293 | 16/18723 | 1.32e-05 | 1.26e-04 | 14 |
GO:200102114 | Thyroid | ATC | negative regulation of response to DNA damage stimulus | 46/6293 | 81/18723 | 1.51e-05 | 1.41e-04 | 46 |
GO:190118415 | Thyroid | ATC | regulation of ERBB signaling pathway | 45/6293 | 79/18723 | 1.68e-05 | 1.55e-04 | 45 |
GO:003278512 | Thyroid | ATC | negative regulation of DNA-templated transcription, elongation | 15/6293 | 18/18723 | 2.06e-05 | 1.85e-04 | 15 |
GO:004354231 | Thyroid | ATC | endothelial cell migration | 127/6293 | 279/18723 | 2.14e-05 | 1.91e-04 | 127 |
GO:001657416 | Thyroid | ATC | histone ubiquitination | 30/6293 | 47/18723 | 2.16e-05 | 1.92e-04 | 30 |
GO:004205814 | Thyroid | ATC | regulation of epidermal growth factor receptor signaling pathway | 42/6293 | 73/18723 | 2.29e-05 | 2.02e-04 | 42 |
GO:190165521 | Thyroid | ATC | cellular response to ketone | 52/6293 | 96/18723 | 2.65e-05 | 2.27e-04 | 52 |
GO:003248113 | Thyroid | ATC | positive regulation of type I interferon production | 35/6293 | 58/18723 | 2.70e-05 | 2.30e-04 | 35 |
GO:004308719 | Thyroid | ATC | regulation of GTPase activity | 153/6293 | 348/18723 | 3.24e-05 | 2.68e-04 | 153 |
GO:000828618 | Thyroid | ATC | insulin receptor signaling pathway | 60/6293 | 116/18723 | 4.20e-05 | 3.40e-04 | 60 |
GO:000651512 | Thyroid | ATC | protein quality control for misfolded or incompletely synthesized proteins | 20/6293 | 28/18723 | 4.82e-05 | 3.85e-04 | 20 |
GO:003090015 | Thyroid | ATC | forebrain development | 164/6293 | 379/18723 | 4.85e-05 | 3.87e-04 | 164 |
GO:000283123 | Thyroid | ATC | regulation of response to biotic stimulus | 144/6293 | 327/18723 | 4.94e-05 | 3.91e-04 | 144 |
GO:003952815 | Thyroid | ATC | cytoplasmic pattern recognition receptor signaling pathway in response to virus | 23/6293 | 34/18723 | 5.15e-05 | 3.99e-04 | 23 |
GO:004214715 | Thyroid | ATC | retrograde transport, endosome to Golgi | 49/6293 | 91/18723 | 5.48e-05 | 4.23e-04 | 49 |
GO:002153712 | Thyroid | ATC | telencephalon development | 113/6293 | 248/18723 | 5.61e-05 | 4.32e-04 | 113 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa040142 | Cervix | CC | Ras signaling pathway | 51/1267 | 236/8465 | 3.55e-03 | 1.34e-02 | 7.91e-03 | 51 |
hsa040109 | Cervix | CC | MAPK signaling pathway | 62/1267 | 302/8465 | 4.89e-03 | 1.67e-02 | 9.86e-03 | 62 |
hsa0401411 | Cervix | CC | Ras signaling pathway | 51/1267 | 236/8465 | 3.55e-03 | 1.34e-02 | 7.91e-03 | 51 |
hsa0401012 | Cervix | CC | MAPK signaling pathway | 62/1267 | 302/8465 | 4.89e-03 | 1.67e-02 | 9.86e-03 | 62 |
hsa01521 | Colorectum | AD | EGFR tyrosine kinase inhibitor resistance | 29/2092 | 79/8465 | 1.15e-02 | 4.24e-02 | 2.71e-02 | 29 |
hsa015211 | Colorectum | AD | EGFR tyrosine kinase inhibitor resistance | 29/2092 | 79/8465 | 1.15e-02 | 4.24e-02 | 2.71e-02 | 29 |
hsa015212 | Colorectum | FAP | EGFR tyrosine kinase inhibitor resistance | 26/1404 | 79/8465 | 2.69e-04 | 2.19e-03 | 1.33e-03 | 26 |
hsa04010 | Colorectum | FAP | MAPK signaling pathway | 68/1404 | 302/8465 | 4.00e-03 | 1.67e-02 | 1.02e-02 | 68 |
hsa015213 | Colorectum | FAP | EGFR tyrosine kinase inhibitor resistance | 26/1404 | 79/8465 | 2.69e-04 | 2.19e-03 | 1.33e-03 | 26 |
hsa040101 | Colorectum | FAP | MAPK signaling pathway | 68/1404 | 302/8465 | 4.00e-03 | 1.67e-02 | 1.02e-02 | 68 |
hsa015214 | Colorectum | CRC | EGFR tyrosine kinase inhibitor resistance | 22/1091 | 79/8465 | 2.89e-04 | 3.45e-03 | 2.34e-03 | 22 |
hsa04014 | Colorectum | CRC | Ras signaling pathway | 49/1091 | 236/8465 | 4.04e-04 | 4.50e-03 | 3.05e-03 | 49 |
hsa040102 | Colorectum | CRC | MAPK signaling pathway | 56/1091 | 302/8465 | 2.76e-03 | 1.77e-02 | 1.20e-02 | 56 |
hsa015215 | Colorectum | CRC | EGFR tyrosine kinase inhibitor resistance | 22/1091 | 79/8465 | 2.89e-04 | 3.45e-03 | 2.34e-03 | 22 |
hsa040141 | Colorectum | CRC | Ras signaling pathway | 49/1091 | 236/8465 | 4.04e-04 | 4.50e-03 | 3.05e-03 | 49 |
hsa040103 | Colorectum | CRC | MAPK signaling pathway | 56/1091 | 302/8465 | 2.76e-03 | 1.77e-02 | 1.20e-02 | 56 |
hsa0152110 | Esophagus | ESCC | EGFR tyrosine kinase inhibitor resistance | 55/4205 | 79/8465 | 2.44e-04 | 8.78e-04 | 4.50e-04 | 55 |
hsa0152115 | Esophagus | ESCC | EGFR tyrosine kinase inhibitor resistance | 55/4205 | 79/8465 | 2.44e-04 | 8.78e-04 | 4.50e-04 | 55 |
hsa015216 | Liver | Cirrhotic | EGFR tyrosine kinase inhibitor resistance | 35/2530 | 79/8465 | 4.50e-03 | 1.70e-02 | 1.05e-02 | 35 |
hsa0152111 | Liver | Cirrhotic | EGFR tyrosine kinase inhibitor resistance | 35/2530 | 79/8465 | 4.50e-03 | 1.70e-02 | 1.05e-02 | 35 |
TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
NF1 | ISLET | Pancreas | Healthy | PWRN1,TMEM260,LRIG3, etc. | 2.22e-02 | ![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.](images/gene_regulatory/Pancreas/Str/TF_Healthy/regulons_activity_in_dotplot.png) |
NF1 | MSC | Prostate | ADJ | CCDC102B,NARS2,CADPS, etc. | 4.55e-02 | ![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.](images/gene_regulatory/Prostate/Str/TF_ADJ/regulons_activity_in_dotplot.png) |
NF1 | MSC | Prostate | BPH | CCDC102B,NARS2,CADPS, etc. | 2.75e-03 | ![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.](images/gene_regulatory/Prostate/Str/TF_BPH/regulons_activity_in_dotplot.png) |
NF1 | FIB | Prostate | Healthy | CCDC102B,NARS2,CADPS, etc. | 7.69e-03 | ![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.](images/gene_regulatory/Prostate/Str/TF_Healthy/regulons_activity_in_dotplot.png) |
NF1 | MSC | Prostate | Tumor | CCDC102B,NARS2,CADPS, etc. | 1.59e-02 | ![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.](images/gene_regulatory/Prostate/Str/TF_Tumor/regulons_activity_in_dotplot.png) |
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 |
NF1 | SNV | Missense_Mutation | | c.1570N>C | p.Glu524Gln | p.E524Q | P21359 | protein_coding | tolerated(0.1) | possibly_damaging(0.732) | TCGA-A2-A0YK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | SD |
NF1 | SNV | Missense_Mutation | novel | c.374N>C | p.Arg125Pro | p.R125P | P21359 | protein_coding | tolerated(0.21) | possibly_damaging(0.567) | TCGA-A7-A6VY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | CR |
NF1 | SNV | Missense_Mutation | | c.4054N>G | p.Ser1352Gly | p.S1352G | P21359 | protein_coding | tolerated(0.21) | benign(0.012) | TCGA-A8-A06X-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
NF1 | SNV | Missense_Mutation | | c.3917G>A | p.Arg1306Gln | p.R1306Q | P21359 | protein_coding | tolerated(0.65) | benign(0.19) | TCGA-A8-A083-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
NF1 | SNV | Missense_Mutation | | c.2147A>T | p.Glu716Val | p.E716V | P21359 | protein_coding | deleterious(0) | probably_damaging(0.983) | TCGA-AC-A23C-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | chemo | CR |
NF1 | SNV | Missense_Mutation | | c.7053N>G | p.Phe2351Leu | p.F2351L | P21359 | protein_coding | tolerated(0.08) | benign(0.063) | TCGA-AN-A0XW-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
NF1 | SNV | Missense_Mutation | | c.3748C>T | p.Arg1250Trp | p.R1250W | P21359 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-AO-A12H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
NF1 | SNV | Missense_Mutation | rs876660206 | c.4341G>C | p.Gln1447His | p.Q1447H | P21359 | protein_coding | deleterious(0.01) | possibly_damaging(0.905) | TCGA-AR-A1AW-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | docetaxel | SD |
NF1 | SNV | Missense_Mutation | novel | c.5713A>C | p.Thr1905Pro | p.T1905P | P21359 | protein_coding | deleterious(0) | probably_damaging(0.961) | TCGA-AR-A1AY-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unspecific | Doxorubicin | SD |
NF1 | SNV | Missense_Mutation | rs774893767 | c.5680G>C | p.Glu1894Gln | p.E1894Q | P21359 | protein_coding | deleterious(0.02) | possibly_damaging(0.867) | TCGA-B6-A0IB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | PD |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | MEK162 | BINIMETINIB | |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | VEMURAFENIB | VEMURAFENIB | 23288408 |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | PD-325901 | | |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | SELUMETINIB | SELUMETINIB | |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | MEK INHIBITOR PD0325901 | | 23171796 |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | JQ1 COMPOUND | | 24373973 |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | SIROLIMUS | SIROLIMUS | 23171796 |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | TRAMETINIB | TRAMETINIB | 29127119 |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | Trametinib | TRAMETINIB | |
4763 | NF1 | CLINICALLY ACTIONABLE, DRUG RESISTANCE | | Cobimetinib | COBIMETINIB | |