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:0010038210 | Thyroid | ATC | response to metal ion | 165/6293 | 373/18723 | 1.07e-05 | 1.05e-04 | 165 |
GO:007259333 | Thyroid | ATC | reactive oxygen species metabolic process | 112/6293 | 239/18723 | 1.34e-05 | 1.28e-04 | 112 |
GO:003235519 | Thyroid | ATC | response to estradiol | 72/6293 | 141/18723 | 1.35e-05 | 1.29e-04 | 72 |
GO:005109022 | Thyroid | ATC | regulation of DNA-binding transcription factor activity | 190/6293 | 440/18723 | 1.49e-05 | 1.39e-04 | 190 |
GO:000963634 | Thyroid | ATC | response to toxic substance | 119/6293 | 262/18723 | 4.30e-05 | 3.48e-04 | 119 |
GO:007207322 | Thyroid | ATC | kidney epithelium development | 68/6293 | 136/18723 | 5.50e-05 | 4.24e-04 | 68 |
GO:000974333 | Thyroid | ATC | response to carbohydrate | 114/6293 | 253/18723 | 9.26e-05 | 6.81e-04 | 114 |
GO:000941613 | Thyroid | ATC | response to light stimulus | 139/6293 | 320/18723 | 1.42e-04 | 9.88e-04 | 139 |
GO:009730528 | Thyroid | ATC | response to alcohol | 113/6293 | 253/18723 | 1.53e-04 | 1.06e-03 | 113 |
GO:007216321 | Thyroid | ATC | mesonephric epithelium development | 48/6293 | 92/18723 | 1.81e-04 | 1.22e-03 | 48 |
GO:007216421 | Thyroid | ATC | mesonephric tubule development | 48/6293 | 92/18723 | 1.81e-04 | 1.22e-03 | 48 |
GO:199074833 | Thyroid | ATC | cellular detoxification | 58/6293 | 116/18723 | 1.88e-04 | 1.26e-03 | 58 |
GO:009723733 | Thyroid | ATC | cellular response to toxic substance | 61/6293 | 124/18723 | 2.31e-04 | 1.49e-03 | 61 |
GO:000165721 | Thyroid | ATC | ureteric bud development | 47/6293 | 91/18723 | 2.85e-04 | 1.82e-03 | 47 |
GO:000182321 | Thyroid | ATC | mesonephros development | 49/6293 | 96/18723 | 3.08e-04 | 1.94e-03 | 49 |
GO:009886932 | Thyroid | ATC | cellular oxidant detoxification | 51/6293 | 101/18723 | 3.29e-04 | 2.05e-03 | 51 |
GO:003428432 | Thyroid | ATC | response to monosaccharide | 100/6293 | 225/18723 | 4.39e-04 | 2.62e-03 | 100 |
GO:00513027 | Thyroid | ATC | regulation of cell division | 80/6293 | 177/18723 | 8.54e-04 | 4.68e-03 | 80 |
GO:000865212 | Thyroid | ATC | cellular amino acid biosynthetic process | 39/6293 | 76/18723 | 1.07e-03 | 5.63e-03 | 39 |
GO:000758418 | Thyroid | ATC | response to nutrient | 78/6293 | 174/18723 | 1.31e-03 | 6.85e-03 | 78 |
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 |