Tissue | Expression Dynamics | Abbreviation |
Breast | ![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/Breast/PAM_pca_on_diff_genes.png) | IDC: Invasive ductal carcinoma |
DCIS: Ductal carcinoma in situ |
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers |
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/PAM_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
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/PAM_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/PAM_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/PAM_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/PAM_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/PAM_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/PAM_pca_on_diff_genes.png) | BPH: Benign Prostatic Hyperplasia |
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/PAM_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:000974312 | Liver | Cirrhotic | response to carbohydrate | 101/4634 | 253/18723 | 6.24e-08 | 1.92e-06 | 101 |
GO:003428412 | Liver | Cirrhotic | response to monosaccharide | 90/4634 | 225/18723 | 2.87e-07 | 7.01e-06 | 90 |
GO:000974612 | Liver | Cirrhotic | response to hexose | 86/4634 | 219/18723 | 1.30e-06 | 2.59e-05 | 86 |
GO:00097497 | Liver | Cirrhotic | response to glucose | 82/4634 | 212/18723 | 4.54e-06 | 7.51e-05 | 82 |
GO:00096155 | Liver | Cirrhotic | response to virus | 126/4634 | 367/18723 | 2.10e-05 | 2.77e-04 | 126 |
GO:00457857 | Liver | Cirrhotic | positive regulation of cell adhesion | 141/4634 | 437/18723 | 2.05e-04 | 1.89e-03 | 141 |
GO:00338651 | Liver | Cirrhotic | nucleoside bisphosphate metabolic process | 50/4634 | 128/18723 | 2.32e-04 | 2.11e-03 | 50 |
GO:00338751 | Liver | Cirrhotic | ribonucleoside bisphosphate metabolic process | 50/4634 | 128/18723 | 2.32e-04 | 2.11e-03 | 50 |
GO:00340321 | Liver | Cirrhotic | purine nucleoside bisphosphate metabolic process | 50/4634 | 128/18723 | 2.32e-04 | 2.11e-03 | 50 |
GO:000664111 | Liver | Cirrhotic | triglyceride metabolic process | 40/4634 | 100/18723 | 5.36e-04 | 4.23e-03 | 40 |
GO:00066371 | Liver | Cirrhotic | acyl-CoA metabolic process | 38/4634 | 96/18723 | 9.23e-04 | 6.57e-03 | 38 |
GO:00353831 | Liver | Cirrhotic | thioester metabolic process | 38/4634 | 96/18723 | 9.23e-04 | 6.57e-03 | 38 |
GO:004887212 | Liver | Cirrhotic | homeostasis of number of cells | 89/4634 | 272/18723 | 1.76e-03 | 1.12e-02 | 89 |
GO:003526411 | Liver | Cirrhotic | multicellular organism growth | 47/4634 | 132/18723 | 3.40e-03 | 1.89e-02 | 47 |
GO:0051607 | Liver | Cirrhotic | defense response to virus | 84/4634 | 265/18723 | 6.02e-03 | 3.00e-02 | 84 |
GO:0140546 | Liver | Cirrhotic | defense response to symbiont | 84/4634 | 265/18723 | 6.02e-03 | 3.00e-02 | 84 |
GO:007259422 | Liver | HCC | establishment of protein localization to organelle | 299/7958 | 422/18723 | 1.06e-32 | 6.10e-30 | 299 |
GO:004427021 | Liver | HCC | cellular nitrogen compound catabolic process | 303/7958 | 451/18723 | 9.76e-27 | 3.64e-24 | 303 |
GO:004670021 | Liver | HCC | heterocycle catabolic process | 299/7958 | 445/18723 | 2.07e-26 | 7.29e-24 | 299 |
GO:190136121 | Liver | HCC | organic cyclic compound catabolic process | 325/7958 | 495/18723 | 6.52e-26 | 2.18e-23 | 325 |
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 |
PAM | SNV | Missense_Mutation | novel | c.371N>T | p.Gly124Val | p.G124V | P19021 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
PAM | SNV | Missense_Mutation | rs752414913 | c.2119C>T | p.Arg707Trp | p.R707W | P19021 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-A8-A09C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PAM | SNV | Missense_Mutation | rs771873156 | c.2710N>A | p.Glu904Lys | p.E904K | P19021 | protein_coding | tolerated(0.06) | benign(0.308) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
PAM | SNV | Missense_Mutation | | c.239N>C | p.Arg80Pro | p.R80P | P19021 | protein_coding | tolerated(0.95) | benign(0.007) | TCGA-BH-A0AW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD |
PAM | SNV | Missense_Mutation | | c.2333A>G | p.His778Arg | p.H778R | P19021 | protein_coding | tolerated(0.34) | benign(0) | TCGA-C8-A1HK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PAM | SNV | Missense_Mutation | novel | c.2433N>C | p.Lys811Asn | p.K811N | P19021 | protein_coding | tolerated(0.05) | benign(0.018) | TCGA-EW-A1PC-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
PAM | deletion | Frame_Shift_Del | novel | c.673delN | p.Asn226IlefsTer16 | p.N226Ifs*16 | P19021 | protein_coding | | | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD |
PAM | SNV | Missense_Mutation | novel | c.304C>T | p.His102Tyr | p.H102Y | P19021 | protein_coding | deleterious(0) | possibly_damaging(0.899) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PAM | SNV | Missense_Mutation | | c.1175N>T | p.Ser392Leu | p.S392L | P19021 | protein_coding | tolerated(0.07) | probably_damaging(0.992) | TCGA-Q1-A73O-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
PAM | SNV | Missense_Mutation | | c.2038N>T | p.Pro680Ser | p.P680S | P19021 | protein_coding | deleterious(0.05) | possibly_damaging(0.632) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |