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/NCL_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/NCL_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/NCL_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/NCL_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/NCL_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/NCL_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
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/NCL_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/NCL_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/NCL_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/NCL_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:005068434 | Thyroid | ATC | regulation of mRNA processing | 97/6293 | 137/18723 | 5.28e-19 | 7.25e-17 | 97 |
GO:004348435 | Thyroid | ATC | regulation of RNA splicing | 100/6293 | 148/18723 | 2.75e-17 | 2.72e-15 | 100 |
GO:0043254210 | Thyroid | ATC | regulation of protein-containing complex assembly | 225/6293 | 428/18723 | 2.72e-16 | 2.33e-14 | 225 |
GO:005082134 | Thyroid | ATC | protein stabilization | 117/6293 | 191/18723 | 3.98e-15 | 2.71e-13 | 117 |
GO:000641735 | Thyroid | ATC | regulation of translation | 236/6293 | 468/18723 | 2.39e-14 | 1.34e-12 | 236 |
GO:004802434 | Thyroid | ATC | regulation of mRNA splicing, via spliceosome | 70/6293 | 101/18723 | 2.29e-13 | 1.09e-11 | 70 |
GO:190331324 | Thyroid | ATC | positive regulation of mRNA metabolic process | 75/6293 | 118/18723 | 2.57e-11 | 8.84e-10 | 75 |
GO:007084926 | Thyroid | ATC | response to epidermal growth factor | 33/6293 | 49/18723 | 1.42e-06 | 1.77e-05 | 33 |
GO:003312033 | Thyroid | ATC | positive regulation of RNA splicing | 26/6293 | 37/18723 | 5.64e-06 | 6.00e-05 | 26 |
GO:007136426 | Thyroid | ATC | cellular response to epidermal growth factor stimulus | 30/6293 | 45/18723 | 5.89e-06 | 6.18e-05 | 30 |
GO:005068522 | Thyroid | ATC | positive regulation of mRNA processing | 23/6293 | 32/18723 | 1.09e-05 | 1.07e-04 | 23 |
GO:003424923 | Thyroid | ATC | negative regulation of cellular amide metabolic process | 121/6293 | 273/18723 | 1.36e-04 | 9.57e-04 | 121 |
GO:001714823 | Thyroid | ATC | negative regulation of translation | 107/6293 | 245/18723 | 6.17e-04 | 3.51e-03 | 107 |
GO:004802633 | Thyroid | ATC | positive regulation of mRNA splicing, via spliceosome | 15/6293 | 22/18723 | 9.63e-04 | 5.13e-03 | 15 |
GO:000635611 | Thyroid | ATC | regulation of transcription by RNA polymerase I | 20/6293 | 34/18723 | 2.22e-03 | 1.04e-02 | 20 |
GO:000636011 | Thyroid | ATC | transcription by RNA polymerase I | 28/6293 | 55/18723 | 5.94e-03 | 2.39e-02 | 28 |
GO:199082318 | Thyroid | ATC | response to leukemia inhibitory factor | 44/6293 | 95/18723 | 6.74e-03 | 2.68e-02 | 44 |
GO:199083017 | Thyroid | ATC | cellular response to leukemia inhibitory factor | 43/6293 | 94/18723 | 9.54e-03 | 3.50e-02 | 43 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0513020 | Cervix | CC | Pathogenic Escherichia coli infection | 63/1267 | 197/8465 | 9.28e-10 | 2.00e-08 | 1.19e-08 | 63 |
hsa05130110 | Cervix | CC | Pathogenic Escherichia coli infection | 63/1267 | 197/8465 | 9.28e-10 | 2.00e-08 | 1.19e-08 | 63 |
hsa05130 | Colorectum | AD | Pathogenic Escherichia coli infection | 79/2092 | 197/8465 | 1.05e-06 | 1.36e-05 | 8.65e-06 | 79 |
hsa051301 | Colorectum | AD | Pathogenic Escherichia coli infection | 79/2092 | 197/8465 | 1.05e-06 | 1.36e-05 | 8.65e-06 | 79 |
hsa051302 | Colorectum | SER | Pathogenic Escherichia coli infection | 60/1580 | 197/8465 | 3.63e-05 | 4.31e-04 | 3.13e-04 | 60 |
hsa051303 | Colorectum | SER | Pathogenic Escherichia coli infection | 60/1580 | 197/8465 | 3.63e-05 | 4.31e-04 | 3.13e-04 | 60 |
hsa051304 | Colorectum | MSS | Pathogenic Escherichia coli infection | 73/1875 | 197/8465 | 1.10e-06 | 1.48e-05 | 9.06e-06 | 73 |
hsa051305 | Colorectum | MSS | Pathogenic Escherichia coli infection | 73/1875 | 197/8465 | 1.10e-06 | 1.48e-05 | 9.06e-06 | 73 |
hsa051306 | Colorectum | MSI-H | Pathogenic Escherichia coli infection | 31/797 | 197/8465 | 2.90e-03 | 2.93e-02 | 2.46e-02 | 31 |
hsa051307 | Colorectum | MSI-H | Pathogenic Escherichia coli infection | 31/797 | 197/8465 | 2.90e-03 | 2.93e-02 | 2.46e-02 | 31 |
hsa051308 | Colorectum | FAP | Pathogenic Escherichia coli infection | 62/1404 | 197/8465 | 1.37e-07 | 3.08e-06 | 1.87e-06 | 62 |
hsa051309 | Colorectum | FAP | Pathogenic Escherichia coli infection | 62/1404 | 197/8465 | 1.37e-07 | 3.08e-06 | 1.87e-06 | 62 |
hsa0513010 | Colorectum | CRC | Pathogenic Escherichia coli infection | 47/1091 | 197/8465 | 1.49e-05 | 3.84e-04 | 2.60e-04 | 47 |
hsa0513011 | Colorectum | CRC | Pathogenic Escherichia coli infection | 47/1091 | 197/8465 | 1.49e-05 | 3.84e-04 | 2.60e-04 | 47 |
hsa0513026 | Endometrium | AEH | Pathogenic Escherichia coli infection | 50/1197 | 197/8465 | 1.72e-05 | 1.86e-04 | 1.36e-04 | 50 |
hsa05130112 | Endometrium | AEH | Pathogenic Escherichia coli infection | 50/1197 | 197/8465 | 1.72e-05 | 1.86e-04 | 1.36e-04 | 50 |
hsa0513027 | Endometrium | EEC | Pathogenic Escherichia coli infection | 51/1237 | 197/8465 | 1.98e-05 | 2.28e-04 | 1.70e-04 | 51 |
hsa0513036 | Endometrium | EEC | Pathogenic Escherichia coli infection | 51/1237 | 197/8465 | 1.98e-05 | 2.28e-04 | 1.70e-04 | 51 |
hsa05130211 | Esophagus | ESCC | Pathogenic Escherichia coli infection | 142/4205 | 197/8465 | 8.21e-11 | 1.06e-09 | 5.42e-10 | 142 |
hsa05130310 | Esophagus | ESCC | Pathogenic Escherichia coli infection | 142/4205 | 197/8465 | 8.21e-11 | 1.06e-09 | 5.42e-10 | 142 |
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 |
NCL | SNV | Missense_Mutation | novel | c.581A>G | p.Asp194Gly | p.D194G | P19338 | protein_coding | tolerated_low_confidence(0.07) | benign(0) | TCGA-A8-A083-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
NCL | SNV | Missense_Mutation | rs769718813 | c.511G>A | p.Glu171Lys | p.E171K | P19338 | protein_coding | tolerated_low_confidence(0.21) | benign(0.003) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
NCL | SNV | Missense_Mutation | | c.94N>A | p.Glu32Lys | p.E32K | P19338 | protein_coding | deleterious_low_confidence(0.01) | benign(0.257) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
NCL | SNV | Missense_Mutation | | c.2063N>A | p.Gly688Glu | p.G688E | P19338 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.999) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
NCL | SNV | Missense_Mutation | | c.2021N>T | p.Gly674Val | p.G674V | P19338 | protein_coding | deleterious_low_confidence(0.02) | probably_damaging(0.989) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
NCL | SNV | Missense_Mutation | novel | c.700G>A | p.Glu234Lys | p.E234K | P19338 | protein_coding | tolerated(0.37) | benign(0.005) | TCGA-BH-A18U-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
NCL | SNV | Missense_Mutation | | c.1789N>T | p.Arg597Trp | p.R597W | P19338 | protein_coding | deleterious(0.03) | probably_damaging(0.983) | TCGA-C8-A27A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
NCL | SNV | Missense_Mutation | | c.871N>G | p.Pro291Ala | p.P291A | P19338 | protein_coding | tolerated(0.07) | benign(0.1) | TCGA-D8-A1J8-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | nolvadex | SD |
NCL | SNV | Missense_Mutation | | c.368N>C | p.Gly123Ala | p.G123A | P19338 | protein_coding | tolerated_low_confidence(0.13) | benign(0.175) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
NCL | SNV | Missense_Mutation | novel | c.790G>A | p.Glu264Lys | p.E264K | P19338 | protein_coding | tolerated(0.05) | benign(0.19) | TCGA-D8-A27G-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |