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/AFMID_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/AFMID_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/AFMID_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/AFMID_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
GC | ![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/GC/AFMID_pca_on_diff_genes.png) | CAG: Chronic atrophic gastritis |
CAG with IM: Chronic atrophic gastritis with intestinal metaplasia |
CSG: Chronic superficial gastritis |
GC: Gastric cancer |
SIM: Severe intestinal metaplasia |
WIM: Wild intestinal metaplasia |
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/AFMID_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0009117 | Colorectum | AD | nucleotide metabolic process | 168/3918 | 489/18723 | 2.20e-12 | 3.36e-10 | 168 |
GO:0006753 | Colorectum | AD | nucleoside phosphate metabolic process | 169/3918 | 497/18723 | 4.99e-12 | 6.98e-10 | 169 |
GO:0044270 | Colorectum | AD | cellular nitrogen compound catabolic process | 147/3918 | 451/18723 | 3.35e-09 | 2.23e-07 | 147 |
GO:0046700 | Colorectum | AD | heterocycle catabolic process | 145/3918 | 445/18723 | 4.37e-09 | 2.84e-07 | 145 |
GO:0019439 | Colorectum | AD | aromatic compound catabolic process | 146/3918 | 467/18723 | 7.48e-08 | 3.84e-06 | 146 |
GO:1901361 | Colorectum | AD | organic cyclic compound catabolic process | 153/3918 | 495/18723 | 8.23e-08 | 4.18e-06 | 153 |
GO:0044282 | Colorectum | AD | small molecule catabolic process | 118/3918 | 376/18723 | 1.05e-06 | 3.55e-05 | 118 |
GO:1901293 | Colorectum | AD | nucleoside phosphate biosynthetic process | 80/3918 | 256/18723 | 6.31e-05 | 1.05e-03 | 80 |
GO:0009165 | Colorectum | AD | nucleotide biosynthetic process | 79/3918 | 254/18723 | 8.33e-05 | 1.30e-03 | 79 |
GO:0016054 | Colorectum | AD | organic acid catabolic process | 73/3918 | 240/18723 | 3.20e-04 | 3.81e-03 | 73 |
GO:0046395 | Colorectum | AD | carboxylic acid catabolic process | 70/3918 | 236/18723 | 9.06e-04 | 8.71e-03 | 70 |
GO:0006520 | Colorectum | AD | cellular amino acid metabolic process | 81/3918 | 284/18723 | 1.37e-03 | 1.19e-02 | 81 |
GO:00442702 | Colorectum | MSS | cellular nitrogen compound catabolic process | 141/3467 | 451/18723 | 2.95e-11 | 3.83e-09 | 141 |
GO:00467002 | Colorectum | MSS | heterocycle catabolic process | 139/3467 | 445/18723 | 4.37e-11 | 5.05e-09 | 139 |
GO:19013612 | Colorectum | MSS | organic cyclic compound catabolic process | 148/3467 | 495/18723 | 3.47e-10 | 3.18e-08 | 148 |
GO:00194392 | Colorectum | MSS | aromatic compound catabolic process | 140/3467 | 467/18723 | 8.56e-10 | 6.85e-08 | 140 |
GO:00091172 | Colorectum | MSS | nucleotide metabolic process | 144/3467 | 489/18723 | 1.87e-09 | 1.35e-07 | 144 |
GO:00067532 | Colorectum | MSS | nucleoside phosphate metabolic process | 145/3467 | 497/18723 | 3.25e-09 | 2.23e-07 | 145 |
GO:19012932 | Colorectum | MSS | nucleoside phosphate biosynthetic process | 71/3467 | 256/18723 | 1.80e-04 | 2.56e-03 | 71 |
GO:00091652 | Colorectum | MSS | nucleotide biosynthetic process | 70/3467 | 254/18723 | 2.44e-04 | 3.34e-03 | 70 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa00380 | Colorectum | FAP | Tryptophan metabolism | 13/1404 | 42/8465 | 1.54e-02 | 4.99e-02 | 3.03e-02 | 13 |
hsa003801 | Colorectum | FAP | Tryptophan metabolism | 13/1404 | 42/8465 | 1.54e-02 | 4.99e-02 | 3.03e-02 | 13 |
hsa012405 | Esophagus | ESCC | Biosynthesis of cofactors | 97/4205 | 153/8465 | 3.88e-04 | 1.35e-03 | 6.94e-04 | 97 |
hsa006306 | Esophagus | ESCC | Glyoxylate and dicarboxylate metabolism | 21/4205 | 30/8465 | 1.95e-02 | 4.35e-02 | 2.23e-02 | 21 |
hsa0124012 | Esophagus | ESCC | Biosynthesis of cofactors | 97/4205 | 153/8465 | 3.88e-04 | 1.35e-03 | 6.94e-04 | 97 |
hsa0063013 | Esophagus | ESCC | Glyoxylate and dicarboxylate metabolism | 21/4205 | 30/8465 | 1.95e-02 | 4.35e-02 | 2.23e-02 | 21 |
hsa006304 | Liver | Cirrhotic | Glyoxylate and dicarboxylate metabolism | 20/2530 | 30/8465 | 3.36e-05 | 2.54e-04 | 1.57e-04 | 20 |
hsa01240 | Liver | Cirrhotic | Biosynthesis of cofactors | 66/2530 | 153/8465 | 3.11e-04 | 1.99e-03 | 1.23e-03 | 66 |
hsa003802 | Liver | Cirrhotic | Tryptophan metabolism | 22/2530 | 42/8465 | 1.85e-03 | 8.37e-03 | 5.16e-03 | 22 |
hsa0063011 | Liver | Cirrhotic | Glyoxylate and dicarboxylate metabolism | 20/2530 | 30/8465 | 3.36e-05 | 2.54e-04 | 1.57e-04 | 20 |
hsa012401 | Liver | Cirrhotic | Biosynthesis of cofactors | 66/2530 | 153/8465 | 3.11e-04 | 1.99e-03 | 1.23e-03 | 66 |
hsa0038011 | Liver | Cirrhotic | Tryptophan metabolism | 22/2530 | 42/8465 | 1.85e-03 | 8.37e-03 | 5.16e-03 | 22 |
hsa012402 | Liver | HCC | Biosynthesis of cofactors | 103/4020 | 153/8465 | 4.67e-07 | 5.05e-06 | 2.81e-06 | 103 |
hsa0063021 | Liver | HCC | Glyoxylate and dicarboxylate metabolism | 24/4020 | 30/8465 | 2.66e-04 | 1.24e-03 | 6.88e-04 | 24 |
hsa012403 | Liver | HCC | Biosynthesis of cofactors | 103/4020 | 153/8465 | 4.67e-07 | 5.05e-06 | 2.81e-06 | 103 |
hsa0063031 | Liver | HCC | Glyoxylate and dicarboxylate metabolism | 24/4020 | 30/8465 | 2.66e-04 | 1.24e-03 | 6.88e-04 | 24 |
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 |
AFMID | SNV | Missense_Mutation | rs374429075 | c.748N>A | p.Glu250Lys | p.E250K | Q63HM1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-FI-A2D5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatinum | PD |
AFMID | SNV | Missense_Mutation | | c.7N>C | p.Asp3His | p.D3H | Q63HM1 | protein_coding | deleterious_low_confidence(0) | benign(0.134) | TCGA-CC-A7IH-01 | Liver | liver hepatocellular carcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
AFMID | SNV | Missense_Mutation | | c.924G>T | p.Gln308His | p.Q308H | Q63HM1 | protein_coding | deleterious_low_confidence(0.02) | possibly_damaging(0.726) | TCGA-44-6778-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
AFMID | SNV | Missense_Mutation | rs532591411 | c.713G>A | p.Arg238His | p.R238H | Q63HM1 | protein_coding | tolerated(0.17) | benign(0.001) | TCGA-78-7155-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | PD |
AFMID | SNV | Missense_Mutation | | c.500N>T | p.Ala167Val | p.A167V | Q63HM1 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-O1-A52J-01 | Lung | lung adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
AFMID | SNV | Missense_Mutation | novel | c.338C>A | p.Pro113Gln | p.P113Q | Q63HM1 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-21-1070-01 | Lung | lung squamous cell carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
AFMID | SNV | Missense_Mutation | novel | c.620A>T | p.Gln207Leu | p.Q207L | Q63HM1 | protein_coding | tolerated(0.43) | benign(0.035) | TCGA-77-A5G6-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | PD |
AFMID | SNV | Missense_Mutation | novel | c.455A>G | p.Tyr152Cys | p.Y152C | Q63HM1 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-CR-7402-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | carboplatin | SD |
AFMID | SNV | Missense_Mutation | novel | c.126G>C | p.Leu42Phe | p.L42F | Q63HM1 | protein_coding | deleterious(0.01) | possibly_damaging(0.494) | TCGA-CV-6441-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | III/IV | Unknown | Unknown | PD |
AFMID | SNV | Missense_Mutation | novel | c.389N>T | p.Pro130Leu | p.P130L | Q63HM1 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CV-7568-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |