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:007232911 | Liver | Cirrhotic | monocarboxylic acid catabolic process | 56/4634 | 122/18723 | 2.87e-07 | 7.01e-06 | 56 |
GO:000906211 | Liver | Cirrhotic | fatty acid catabolic process | 48/4634 | 100/18723 | 3.87e-07 | 9.13e-06 | 48 |
GO:004873212 | Liver | Cirrhotic | gland development | 154/4634 | 436/18723 | 4.03e-07 | 9.42e-06 | 154 |
GO:000663512 | Liver | Cirrhotic | fatty acid beta-oxidation | 38/4634 | 74/18723 | 7.41e-07 | 1.57e-05 | 38 |
GO:00704827 | Liver | Cirrhotic | response to oxygen levels | 125/4634 | 347/18723 | 1.55e-06 | 3.02e-05 | 125 |
GO:00725937 | Liver | Cirrhotic | reactive oxygen species metabolic process | 92/4634 | 239/18723 | 1.57e-06 | 3.03e-05 | 92 |
GO:009730512 | Liver | Cirrhotic | response to alcohol | 96/4634 | 253/18723 | 1.97e-06 | 3.65e-05 | 96 |
GO:00090631 | Liver | Cirrhotic | cellular amino acid catabolic process | 49/4634 | 110/18723 | 4.47e-06 | 7.42e-05 | 49 |
GO:004668612 | Liver | Cirrhotic | response to cadmium ion | 34/4634 | 68/18723 | 6.04e-06 | 9.74e-05 | 34 |
GO:004424212 | Liver | Cirrhotic | cellular lipid catabolic process | 82/4634 | 214/18723 | 6.91e-06 | 1.08e-04 | 82 |
GO:000652011 | Liver | Cirrhotic | cellular amino acid metabolic process | 103/4634 | 284/18723 | 8.88e-06 | 1.30e-04 | 103 |
GO:000908111 | Liver | Cirrhotic | branched-chain amino acid metabolic process | 14/4634 | 19/18723 | 1.00e-05 | 1.45e-04 | 14 |
GO:007054211 | Liver | Cirrhotic | response to fatty acid | 32/4634 | 64/18723 | 1.13e-05 | 1.60e-04 | 32 |
GO:00362937 | Liver | Cirrhotic | response to decreased oxygen levels | 113/4634 | 322/18723 | 1.87e-05 | 2.52e-04 | 113 |
GO:001604212 | Liver | Cirrhotic | lipid catabolic process | 112/4634 | 320/18723 | 2.31e-05 | 3.03e-04 | 112 |
GO:00016667 | Liver | Cirrhotic | response to hypoxia | 108/4634 | 307/18723 | 2.51e-05 | 3.26e-04 | 108 |
GO:003286811 | Liver | Cirrhotic | response to insulin | 95/4634 | 264/18723 | 2.77e-05 | 3.54e-04 | 95 |
GO:000756812 | Liver | Cirrhotic | aging | 117/4634 | 339/18723 | 3.13e-05 | 3.91e-04 | 117 |
GO:000758411 | Liver | Cirrhotic | response to nutrient | 67/4634 | 174/18723 | 3.83e-05 | 4.59e-04 | 67 |
GO:00987547 | Liver | Cirrhotic | detoxification | 60/4634 | 152/18723 | 4.09e-05 | 4.86e-04 | 60 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05208 | Colorectum | AD | Chemical carcinogenesis - reactive oxygen species | 126/2092 | 223/8465 | 1.01e-24 | 1.68e-22 | 1.07e-22 | 126 |
hsa05014 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
hsa05022 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
hsa01200 | Colorectum | AD | Carbon metabolism | 55/2092 | 115/8465 | 5.53e-08 | 8.42e-07 | 5.37e-07 | 55 |
hsa04213 | Colorectum | AD | Longevity regulating pathway - multiple species | 27/2092 | 62/8465 | 8.72e-04 | 5.96e-03 | 3.80e-03 | 27 |
hsa04211 | Colorectum | AD | Longevity regulating pathway | 33/2092 | 89/8465 | 6.15e-03 | 2.68e-02 | 1.71e-02 | 33 |
hsa00630 | Colorectum | AD | Glyoxylate and dicarboxylate metabolism | 14/2092 | 30/8465 | 7.25e-03 | 2.97e-02 | 1.89e-02 | 14 |
hsa052081 | Colorectum | AD | Chemical carcinogenesis - reactive oxygen species | 126/2092 | 223/8465 | 1.01e-24 | 1.68e-22 | 1.07e-22 | 126 |
hsa050141 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
hsa050221 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
hsa012001 | Colorectum | AD | Carbon metabolism | 55/2092 | 115/8465 | 5.53e-08 | 8.42e-07 | 5.37e-07 | 55 |
hsa042131 | Colorectum | AD | Longevity regulating pathway - multiple species | 27/2092 | 62/8465 | 8.72e-04 | 5.96e-03 | 3.80e-03 | 27 |
hsa042111 | Colorectum | AD | Longevity regulating pathway | 33/2092 | 89/8465 | 6.15e-03 | 2.68e-02 | 1.71e-02 | 33 |
hsa006301 | Colorectum | AD | Glyoxylate and dicarboxylate metabolism | 14/2092 | 30/8465 | 7.25e-03 | 2.97e-02 | 1.89e-02 | 14 |
hsa050222 | Colorectum | SER | Pathways of neurodegeneration - multiple diseases | 168/1580 | 476/8465 | 6.23e-19 | 2.07e-17 | 1.50e-17 | 168 |
hsa050142 | Colorectum | SER | Amyotrophic lateral sclerosis | 138/1580 | 364/8465 | 9.89e-19 | 2.99e-17 | 2.17e-17 | 138 |
hsa050223 | Colorectum | SER | Pathways of neurodegeneration - multiple diseases | 168/1580 | 476/8465 | 6.23e-19 | 2.07e-17 | 1.50e-17 | 168 |
hsa050143 | Colorectum | SER | Amyotrophic lateral sclerosis | 138/1580 | 364/8465 | 9.89e-19 | 2.99e-17 | 2.17e-17 | 138 |
hsa052084 | Colorectum | MSS | Chemical carcinogenesis - reactive oxygen species | 118/1875 | 223/8465 | 2.71e-24 | 4.54e-22 | 2.78e-22 | 118 |
hsa050224 | Colorectum | MSS | Pathways of neurodegeneration - multiple diseases | 192/1875 | 476/8465 | 2.79e-20 | 1.04e-18 | 6.36e-19 | 192 |
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 |