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/LPP_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/LPP_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
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/LPP_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/LPP_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/LPP_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/LPP_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/LPP_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/LPP_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/LPP_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/LPP_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/LPP_pca_on_diff_genes.png) | BPH: Benign Prostatic Hyperplasia |
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/LPP_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/LPP_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:000762321 | Liver | HCC | circadian rhythm | 117/7958 | 210/18723 | 7.29e-05 | 6.54e-04 | 117 |
GO:000689011 | Liver | HCC | retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum | 36/7958 | 52/18723 | 8.79e-05 | 7.66e-04 | 36 |
GO:000975521 | Liver | HCC | hormone-mediated signaling pathway | 106/7958 | 190/18723 | 1.45e-04 | 1.17e-03 | 106 |
GO:003052121 | Liver | HCC | androgen receptor signaling pathway | 31/7958 | 44/18723 | 1.63e-04 | 1.30e-03 | 31 |
GO:006104122 | Liver | HCC | regulation of wound healing | 78/7958 | 134/18723 | 1.73e-04 | 1.36e-03 | 78 |
GO:190303421 | Liver | HCC | regulation of response to wounding | 94/7958 | 167/18723 | 2.19e-04 | 1.66e-03 | 94 |
GO:003410912 | Liver | HCC | homotypic cell-cell adhesion | 55/7958 | 90/18723 | 2.81e-04 | 2.02e-03 | 55 |
GO:004851121 | Liver | HCC | rhythmic process | 156/7958 | 298/18723 | 3.54e-04 | 2.46e-03 | 156 |
GO:009030321 | Liver | HCC | positive regulation of wound healing | 38/7958 | 59/18723 | 5.61e-04 | 3.61e-03 | 38 |
GO:00510902 | Liver | HCC | regulation of DNA-binding transcription factor activity | 220/7958 | 440/18723 | 8.04e-04 | 4.82e-03 | 220 |
GO:007030222 | Liver | HCC | regulation of stress-activated protein kinase signaling cascade | 105/7958 | 195/18723 | 8.79e-04 | 5.20e-03 | 105 |
GO:190303621 | Liver | HCC | positive regulation of response to wounding | 44/7958 | 72/18723 | 1.10e-03 | 6.32e-03 | 44 |
GO:0006665 | Liver | HCC | sphingolipid metabolic process | 85/7958 | 155/18723 | 1.27e-03 | 6.92e-03 | 85 |
GO:1902806 | Liver | HCC | regulation of cell cycle G1/S phase transition | 91/7958 | 168/18723 | 1.47e-03 | 7.79e-03 | 91 |
GO:0046467 | Liver | HCC | membrane lipid biosynthetic process | 78/7958 | 142/18723 | 1.85e-03 | 9.46e-03 | 78 |
GO:003287222 | Liver | HCC | regulation of stress-activated MAPK cascade | 102/7958 | 192/18723 | 1.86e-03 | 9.49e-03 | 102 |
GO:004578512 | Liver | HCC | positive regulation of cell adhesion | 215/7958 | 437/18723 | 2.53e-03 | 1.22e-02 | 215 |
GO:003361911 | Liver | HCC | membrane protein proteolysis | 35/7958 | 57/18723 | 3.08e-03 | 1.43e-02 | 35 |
GO:000725412 | Liver | HCC | JNK cascade | 89/7958 | 167/18723 | 3.09e-03 | 1.44e-02 | 89 |
GO:00072292 | Liver | HCC | integrin-mediated signaling pathway | 60/7958 | 107/18723 | 3.15e-03 | 1.46e-02 | 60 |
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 |
LPP | SNV | Missense_Mutation | rs749505857 | c.1396G>A | p.Glu466Lys | p.E466K | | protein_coding | deleterious(0) | possibly_damaging(0.889) | TCGA-5L-AAT0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
LPP | SNV | Missense_Mutation | | c.922N>C | p.Gly308Arg | p.G308R | | protein_coding | tolerated(0.11) | possibly_damaging(0.818) | TCGA-A1-A0SH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tc | SD |
LPP | SNV | Missense_Mutation | rs756003756 | c.1457G>A | p.Arg486Gln | p.R486Q | | protein_coding | deleterious(0) | possibly_damaging(0.74) | TCGA-A1-A0SM-01 | Breast | breast invasive carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
LPP | SNV | Missense_Mutation | | c.254N>G | p.Ser85Cys | p.S85C | | protein_coding | tolerated(0.05) | benign(0.276) | TCGA-A7-A26G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | SD |
LPP | SNV | Missense_Mutation | | c.1834N>G | p.Leu612Val | p.L612V | | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.974) | TCGA-A8-A083-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LPP | SNV | Missense_Mutation | novel | c.1576N>A | p.Glu526Lys | p.E526K | | protein_coding | deleterious(0) | possibly_damaging(0.57) | TCGA-A8-A0A7-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LPP | SNV | Missense_Mutation | novel | c.1274N>T | p.Gly425Val | p.G425V | | protein_coding | deleterious(0) | possibly_damaging(0.874) | TCGA-AC-A2QH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
LPP | SNV | Missense_Mutation | | c.1391N>G | p.Tyr464Cys | p.Y464C | | protein_coding | deleterious(0) | probably_damaging(0.95) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD |
LPP | SNV | Missense_Mutation | novel | c.452N>G | p.Ser151Cys | p.S151C | | protein_coding | deleterious(0.02) | possibly_damaging(0.885) | TCGA-PE-A5DE-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
LPP | SNV | Missense_Mutation | | c.1751N>A | p.Cys584Tyr | p.C584Y | | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |