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/PTPRF_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/PTPRF_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/PTPRF_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/PTPRF_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/PTPRF_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/PTPRF_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/PTPRF_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/PTPRF_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
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/PTPRF_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/PTPRF_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/PTPRF_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/PTPRF_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:00310991 | Colorectum | MSI-H | regeneration | 25/1319 | 198/18723 | 3.27e-03 | 3.99e-02 | 25 |
GO:00615643 | Colorectum | FAP | axon development | 106/2622 | 467/18723 | 1.98e-07 | 1.21e-05 | 106 |
GO:00109753 | Colorectum | FAP | regulation of neuron projection development | 102/2622 | 445/18723 | 2.04e-07 | 1.24e-05 | 102 |
GO:00163113 | Colorectum | FAP | dephosphorylation | 95/2622 | 417/18723 | 7.07e-07 | 3.32e-05 | 95 |
GO:00064704 | Colorectum | FAP | protein dephosphorylation | 69/2622 | 281/18723 | 1.47e-06 | 6.39e-05 | 69 |
GO:00510984 | Colorectum | FAP | regulation of binding | 81/2622 | 363/18723 | 1.04e-05 | 2.97e-04 | 81 |
GO:00508083 | Colorectum | FAP | synapse organization | 91/2622 | 426/18723 | 1.90e-05 | 4.74e-04 | 91 |
GO:19030341 | Colorectum | FAP | regulation of response to wounding | 41/2622 | 167/18723 | 1.86e-04 | 2.74e-03 | 41 |
GO:00433934 | Colorectum | FAP | regulation of protein binding | 46/2622 | 196/18723 | 2.40e-04 | 3.35e-03 | 46 |
GO:0035335 | Colorectum | FAP | peptidyl-tyrosine dephosphorylation | 23/2622 | 97/18723 | 6.95e-03 | 4.26e-02 | 23 |
GO:00510985 | Colorectum | CRC | regulation of binding | 72/2078 | 363/18723 | 6.43e-07 | 4.50e-05 | 72 |
GO:00163114 | Colorectum | CRC | dephosphorylation | 79/2078 | 417/18723 | 1.27e-06 | 7.21e-05 | 79 |
GO:00615644 | Colorectum | CRC | axon development | 86/2078 | 467/18723 | 1.48e-06 | 8.12e-05 | 86 |
GO:00109754 | Colorectum | CRC | regulation of neuron projection development | 82/2078 | 445/18723 | 2.51e-06 | 1.19e-04 | 82 |
GO:00064705 | Colorectum | CRC | protein dephosphorylation | 57/2078 | 281/18723 | 4.49e-06 | 1.87e-04 | 57 |
GO:00433935 | Colorectum | CRC | regulation of protein binding | 42/2078 | 196/18723 | 2.01e-05 | 5.90e-04 | 42 |
GO:00508084 | Colorectum | CRC | synapse organization | 71/2078 | 426/18723 | 3.02e-04 | 4.76e-03 | 71 |
GO:00511003 | Colorectum | CRC | negative regulation of binding | 30/2078 | 162/18723 | 3.36e-03 | 2.87e-02 | 30 |
GO:005109817 | Endometrium | EEC | regulation of binding | 83/2168 | 363/18723 | 6.72e-10 | 6.61e-08 | 83 |
GO:006156412 | Endometrium | EEC | axon development | 93/2168 | 467/18723 | 9.60e-08 | 4.69e-06 | 93 |
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 |
PTPRF | SNV | Missense_Mutation | novel | c.5273N>G | p.Ser1758Cys | p.S1758C | P10586 | protein_coding | deleterious(0.02) | probably_damaging(0.999) | TCGA-5L-AAT1-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Hormone Therapy | letrozol | SD |
PTPRF | SNV | Missense_Mutation | | c.4751N>A | p.Arg1584Gln | p.R1584Q | P10586 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-A8-A085-01 | Breast | breast invasive carcinoma | Male | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
PTPRF | SNV | Missense_Mutation | | c.5368G>A | p.Gly1790Arg | p.G1790R | P10586 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
PTPRF | SNV | Missense_Mutation | rs565543436 | c.2468N>A | p.Arg823Gln | p.R823Q | P10586 | protein_coding | tolerated(0.12) | benign(0.36) | TCGA-AN-A0AK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PTPRF | SNV | Missense_Mutation | rs767075536 | c.2671N>T | p.Arg891Trp | p.R891W | P10586 | protein_coding | tolerated(0.06) | possibly_damaging(0.863) | TCGA-BH-A0HA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PTPRF | SNV | Missense_Mutation | | c.4015N>A | p.Asp1339Asn | p.D1339N | P10586 | protein_coding | tolerated(0.17) | probably_damaging(0.911) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD |
PTPRF | SNV | Missense_Mutation | | c.5710N>A | p.His1904Asn | p.H1904N | P10586 | protein_coding | deleterious(0.02) | probably_damaging(0.987) | TCGA-BH-A0HP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | doxorubicin | SD |
PTPRF | SNV | Missense_Mutation | | c.5201N>C | p.Ile1734Thr | p.I1734T | P10586 | protein_coding | deleterious(0.01) | probably_damaging(1) | TCGA-BH-A1FU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
PTPRF | SNV | Missense_Mutation | novel | c.64N>C | p.Gly22Arg | p.G22R | P10586 | protein_coding | tolerated_low_confidence(0.47) | benign(0.063) | TCGA-BH-A5IZ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
PTPRF | SNV | Missense_Mutation | rs367652888 | c.2492N>T | p.Thr831Met | p.T831M | P10586 | protein_coding | tolerated(0.09) | probably_damaging(1) | TCGA-C8-A134-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |