Tissue | Expression Dynamics | Abbreviation |
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/CAT_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/CAT_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal 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/CAT_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/CAT_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/CAT_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/CAT_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
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/CAT_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/CAT_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:004586210 | Cervix | CC | positive regulation of proteolysis | 95/2311 | 372/18723 | 1.84e-12 | 6.86e-10 | 95 |
GO:190589710 | Cervix | CC | regulation of response to endoplasmic reticulum stress | 27/2311 | 82/18723 | 9.24e-07 | 3.25e-05 | 27 |
GO:004887210 | Cervix | CC | homeostasis of number of cells | 61/2311 | 272/18723 | 2.17e-06 | 6.55e-05 | 61 |
GO:003497610 | Cervix | CC | response to endoplasmic reticulum stress | 57/2311 | 256/18723 | 5.81e-06 | 1.42e-04 | 57 |
GO:190357310 | Cervix | CC | negative regulation of response to endoplasmic reticulum stress | 17/2311 | 44/18723 | 8.57e-06 | 1.97e-04 | 17 |
GO:00507273 | Cervix | CC | regulation of inflammatory response | 75/2311 | 386/18723 | 3.95e-05 | 6.18e-04 | 75 |
GO:00069846 | Cervix | CC | ER-nucleus signaling pathway | 16/2311 | 46/18723 | 7.12e-05 | 9.90e-04 | 16 |
GO:00516048 | Cervix | CC | protein maturation | 56/2311 | 294/18723 | 5.90e-04 | 5.59e-03 | 56 |
GO:00321022 | Cervix | CC | negative regulation of response to external stimulus | 75/2311 | 420/18723 | 5.96e-04 | 5.61e-03 | 75 |
GO:0031348 | Cervix | CC | negative regulation of defense response | 48/2311 | 258/18723 | 2.30e-03 | 1.65e-02 | 48 |
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:0015980 | Colorectum | AD | energy derivation by oxidation of organic compounds | 143/3918 | 318/18723 | 2.78e-22 | 2.49e-19 | 143 |
GO:0009150 | Colorectum | AD | purine ribonucleotide metabolic process | 142/3918 | 368/18723 | 4.29e-15 | 1.17e-12 | 142 |
GO:0006163 | Colorectum | AD | purine nucleotide metabolic process | 149/3918 | 396/18723 | 1.08e-14 | 2.80e-12 | 149 |
GO:0072521 | Colorectum | AD | purine-containing compound metabolic process | 153/3918 | 416/18723 | 4.34e-14 | 1.01e-11 | 153 |
GO:0009259 | Colorectum | AD | ribonucleotide metabolic process | 144/3918 | 385/18723 | 5.25e-14 | 1.13e-11 | 144 |
GO:0019693 | Colorectum | AD | ribose phosphate metabolic process | 145/3918 | 396/18723 | 3.01e-13 | 5.71e-11 | 145 |
GO:0009117 | Colorectum | AD | nucleotide metabolic process | 168/3918 | 489/18723 | 2.20e-12 | 3.36e-10 | 168 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0502238 | Esophagus | ESCC | Pathways of neurodegeneration - multiple diseases | 318/4205 | 476/8465 | 6.10e-15 | 2.04e-13 | 1.05e-13 | 318 |
hsa0406814 | Esophagus | ESCC | FoxO signaling pathway | 89/4205 | 131/8465 | 1.56e-05 | 7.98e-05 | 4.09e-05 | 89 |
hsa0120033 | Esophagus | ESCC | Carbon metabolism | 79/4205 | 115/8465 | 2.50e-05 | 1.21e-04 | 6.22e-05 | 79 |
hsa0414612 | Esophagus | ESCC | Peroxisome | 55/4205 | 82/8465 | 1.04e-03 | 3.27e-03 | 1.68e-03 | 55 |
hsa0421115 | Esophagus | ESCC | Longevity regulating pathway | 58/4205 | 89/8465 | 2.19e-03 | 6.16e-03 | 3.16e-03 | 58 |
hsa0063013 | Esophagus | ESCC | Glyoxylate and dicarboxylate metabolism | 21/4205 | 30/8465 | 1.95e-02 | 4.35e-02 | 2.23e-02 | 21 |
hsa0501414 | Liver | Cirrhotic | Amyotrophic lateral sclerosis | 187/2530 | 364/8465 | 1.56e-18 | 6.50e-17 | 4.01e-17 | 187 |
hsa0520822 | Liver | Cirrhotic | Chemical carcinogenesis - reactive oxygen species | 121/2530 | 223/8465 | 1.35e-14 | 4.08e-13 | 2.52e-13 | 121 |
hsa0502214 | Liver | Cirrhotic | Pathways of neurodegeneration - multiple diseases | 217/2530 | 476/8465 | 7.30e-14 | 2.03e-12 | 1.25e-12 | 217 |
hsa0120021 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
hsa006304 | Liver | Cirrhotic | Glyoxylate and dicarboxylate metabolism | 20/2530 | 30/8465 | 3.36e-05 | 2.54e-04 | 1.57e-04 | 20 |
hsa003802 | Liver | Cirrhotic | Tryptophan metabolism | 22/2530 | 42/8465 | 1.85e-03 | 8.37e-03 | 5.16e-03 | 22 |
hsa041462 | Liver | Cirrhotic | Peroxisome | 36/2530 | 82/8465 | 4.79e-03 | 1.74e-02 | 1.07e-02 | 36 |
hsa040682 | Liver | Cirrhotic | FoxO signaling pathway | 52/2530 | 131/8465 | 9.98e-03 | 3.32e-02 | 2.05e-02 | 52 |
hsa042118 | Liver | Cirrhotic | Longevity regulating pathway | 37/2530 | 89/8465 | 1.22e-02 | 3.89e-02 | 2.40e-02 | 37 |
hsa0501415 | Liver | Cirrhotic | Amyotrophic lateral sclerosis | 187/2530 | 364/8465 | 1.56e-18 | 6.50e-17 | 4.01e-17 | 187 |
hsa0520832 | Liver | Cirrhotic | Chemical carcinogenesis - reactive oxygen species | 121/2530 | 223/8465 | 1.35e-14 | 4.08e-13 | 2.52e-13 | 121 |
hsa0502215 | Liver | Cirrhotic | Pathways of neurodegeneration - multiple diseases | 217/2530 | 476/8465 | 7.30e-14 | 2.03e-12 | 1.25e-12 | 217 |
hsa0120031 | Liver | Cirrhotic | Carbon metabolism | 64/2530 | 115/8465 | 6.37e-09 | 1.18e-07 | 7.26e-08 | 64 |
hsa0063011 | Liver | Cirrhotic | Glyoxylate and dicarboxylate metabolism | 20/2530 | 30/8465 | 3.36e-05 | 2.54e-04 | 1.57e-04 | 20 |
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 |
CAT | SNV | Missense_Mutation | rs573379158 | c.1559N>T | p.Ala520Val | p.A520V | P04040 | protein_coding | tolerated_low_confidence(0.11) | benign(0) | TCGA-E2-A153-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD |
CAT | insertion | Nonsense_Mutation | novel | c.883_884insTGTATTCTATTATTTGAATTTTTACACTC | p.Asn295MetfsTer6 | p.N295Mfs*6 | P04040 | protein_coding | | | TCGA-A8-A07L-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | | CR |
CAT | SNV | Missense_Mutation | rs756388518 | c.385N>T | p.Pro129Ser | p.P129S | P04040 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
CAT | SNV | Missense_Mutation | rs573379158 | c.1559C>T | p.Ala520Val | p.A520V | P04040 | protein_coding | tolerated_low_confidence(0.11) | benign(0) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
CAT | SNV | Missense_Mutation | | c.988N>A | p.Glu330Lys | p.E330K | P04040 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-FU-A23K-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD |
CAT | SNV | Missense_Mutation | | c.415N>A | p.Glu139Lys | p.E139K | P04040 | protein_coding | deleterious(0.01) | possibly_damaging(0.552) | TCGA-VS-A9UP-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD |
CAT | SNV | Missense_Mutation | rs752948472 | c.380N>A | p.Arg127Gln | p.R127Q | P04040 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CAT | SNV | Missense_Mutation | rs777189700 | c.1145N>A | p.Arg382Gln | p.R382Q | P04040 | protein_coding | tolerated(0.26) | benign(0.015) | TCGA-AZ-4313-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CAT | SNV | Missense_Mutation | rs778007071 | c.749N>T | p.Ala250Val | p.A250V | P04040 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AZ-6598-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CAT | SNV | Missense_Mutation | novel | c.468N>T | p.Arg156Ser | p.R156S | P04040 | protein_coding | deleterious(0.02) | possibly_damaging(0.631) | TCGA-AG-3892-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |