Tissue | Expression Dynamics | Abbreviation |
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/PDE4D_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/PDE4D_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/PDE4D_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/PDE4D_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/PDE4D_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/PDE4D_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/PDE4D_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/PDE4D_pca_on_diff_genes.png) | AAH: Atypical adenomatous hyperplasia |
AIS: Adenocarcinoma in situ |
IAC: Invasive lung adenocarcinoma |
MIA: Minimally invasive adenocarcinoma |
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/PDE4D_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/PDE4D_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/PDE4D_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:000915011 | Stomach | CAG with IM | purine ribonucleotide metabolic process | 48/1050 | 368/18723 | 4.36e-08 | 3.32e-06 | 48 |
GO:000616311 | Stomach | CAG with IM | purine nucleotide metabolic process | 50/1050 | 396/18723 | 6.52e-08 | 4.63e-06 | 50 |
GO:000925911 | Stomach | CAG with IM | ribonucleotide metabolic process | 48/1050 | 385/18723 | 1.76e-07 | 1.16e-05 | 48 |
GO:007252111 | Stomach | CAG with IM | purine-containing compound metabolic process | 50/1050 | 416/18723 | 3.04e-07 | 1.82e-05 | 50 |
GO:001969311 | Stomach | CAG with IM | ribose phosphate metabolic process | 48/1050 | 396/18723 | 4.08e-07 | 2.34e-05 | 48 |
GO:000911711 | Stomach | CAG with IM | nucleotide metabolic process | 54/1050 | 489/18723 | 1.52e-06 | 7.14e-05 | 54 |
GO:000675311 | Stomach | CAG with IM | nucleoside phosphate metabolic process | 54/1050 | 497/18723 | 2.49e-06 | 1.07e-04 | 54 |
GO:000206411 | Stomach | CAG with IM | epithelial cell development | 29/1050 | 220/18723 | 1.64e-05 | 5.16e-04 | 29 |
GO:00512351 | Stomach | CAG with IM | maintenance of location | 38/1050 | 327/18723 | 1.71e-05 | 5.34e-04 | 38 |
GO:003004811 | Stomach | CAG with IM | actin filament-based movement | 20/1050 | 127/18723 | 2.61e-05 | 7.39e-04 | 20 |
GO:005165111 | Stomach | CAG with IM | maintenance of location in cell | 27/1050 | 214/18723 | 6.85e-05 | 1.66e-03 | 27 |
GO:006102811 | Stomach | CAG with IM | establishment of endothelial barrier | 9/1050 | 46/18723 | 8.92e-04 | 1.17e-02 | 9 |
GO:00018191 | Stomach | CAG with IM | positive regulation of cytokine production | 43/1050 | 467/18723 | 9.84e-04 | 1.27e-02 | 43 |
GO:00027641 | Stomach | CAG with IM | immune response-regulating signaling pathway | 43/1050 | 468/18723 | 1.03e-03 | 1.29e-02 | 43 |
GO:000315811 | Stomach | CAG with IM | endothelium development | 17/1050 | 136/18723 | 1.59e-03 | 1.76e-02 | 17 |
GO:004593611 | Stomach | CAG with IM | negative regulation of phosphate metabolic process | 40/1050 | 441/18723 | 1.91e-03 | 2.02e-02 | 40 |
GO:001056311 | Stomach | CAG with IM | negative regulation of phosphorus metabolic process | 40/1050 | 442/18723 | 1.99e-03 | 2.09e-02 | 40 |
GO:19018441 | Stomach | CAG with IM | regulation of cell communication by electrical coupling involved in cardiac conduction | 4/1050 | 11/18723 | 2.36e-03 | 2.35e-02 | 4 |
GO:008600311 | Stomach | CAG with IM | cardiac muscle cell contraction | 11/1050 | 73/18723 | 2.38e-03 | 2.37e-02 | 11 |
GO:008600411 | Stomach | CAG with IM | regulation of cardiac muscle cell contraction | 7/1050 | 34/18723 | 2.42e-03 | 2.39e-02 | 7 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0492812 | Cervix | CC | Parathyroid hormone synthesis, secretion and action | 27/1267 | 106/8465 | 3.12e-03 | 1.19e-02 | 7.03e-03 | 27 |
hsa0492813 | Cervix | CC | Parathyroid hormone synthesis, secretion and action | 27/1267 | 106/8465 | 3.12e-03 | 1.19e-02 | 7.03e-03 | 27 |
hsa04928 | Colorectum | AD | Parathyroid hormone synthesis, secretion and action | 38/2092 | 106/8465 | 6.60e-03 | 2.77e-02 | 1.76e-02 | 38 |
hsa049281 | Colorectum | AD | Parathyroid hormone synthesis, secretion and action | 38/2092 | 106/8465 | 6.60e-03 | 2.77e-02 | 1.76e-02 | 38 |
hsa049282 | Colorectum | SER | Parathyroid hormone synthesis, secretion and action | 31/1580 | 106/8465 | 5.20e-03 | 3.28e-02 | 2.38e-02 | 31 |
hsa049283 | Colorectum | SER | Parathyroid hormone synthesis, secretion and action | 31/1580 | 106/8465 | 5.20e-03 | 3.28e-02 | 2.38e-02 | 31 |
hsa049284 | Colorectum | MSS | Parathyroid hormone synthesis, secretion and action | 37/1875 | 106/8465 | 1.72e-03 | 9.13e-03 | 5.59e-03 | 37 |
hsa049285 | Colorectum | MSS | Parathyroid hormone synthesis, secretion and action | 37/1875 | 106/8465 | 1.72e-03 | 9.13e-03 | 5.59e-03 | 37 |
hsa049286 | Colorectum | FAP | Parathyroid hormone synthesis, secretion and action | 29/1404 | 106/8465 | 3.37e-03 | 1.44e-02 | 8.77e-03 | 29 |
hsa04024 | Colorectum | FAP | cAMP signaling pathway | 51/1404 | 225/8465 | 1.02e-02 | 3.68e-02 | 2.24e-02 | 51 |
hsa049287 | Colorectum | FAP | Parathyroid hormone synthesis, secretion and action | 29/1404 | 106/8465 | 3.37e-03 | 1.44e-02 | 8.77e-03 | 29 |
hsa040241 | Colorectum | FAP | cAMP signaling pathway | 51/1404 | 225/8465 | 1.02e-02 | 3.68e-02 | 2.24e-02 | 51 |
hsa040242 | Colorectum | CRC | cAMP signaling pathway | 47/1091 | 225/8465 | 4.57e-04 | 4.77e-03 | 3.23e-03 | 47 |
hsa049288 | Colorectum | CRC | Parathyroid hormone synthesis, secretion and action | 24/1091 | 106/8465 | 3.71e-03 | 2.29e-02 | 1.55e-02 | 24 |
hsa040243 | Colorectum | CRC | cAMP signaling pathway | 47/1091 | 225/8465 | 4.57e-04 | 4.77e-03 | 3.23e-03 | 47 |
hsa049289 | Colorectum | CRC | Parathyroid hormone synthesis, secretion and action | 24/1091 | 106/8465 | 3.71e-03 | 2.29e-02 | 1.55e-02 | 24 |
hsa0492816 | Esophagus | ESCC | Parathyroid hormone synthesis, secretion and action | 66/4205 | 106/8465 | 5.86e-03 | 1.47e-02 | 7.51e-03 | 66 |
hsa0492817 | Esophagus | ESCC | Parathyroid hormone synthesis, secretion and action | 66/4205 | 106/8465 | 5.86e-03 | 1.47e-02 | 7.51e-03 | 66 |
hsa0492810 | Lung | IAC | Parathyroid hormone synthesis, secretion and action | 26/1053 | 106/8465 | 4.34e-04 | 4.03e-03 | 2.68e-03 | 26 |
hsa0492811 | Lung | IAC | Parathyroid hormone synthesis, secretion and action | 26/1053 | 106/8465 | 4.34e-04 | 4.03e-03 | 2.68e-03 | 26 |
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 |
PDE4D | SNV | Missense_Mutation | | c.647T>C | p.Ile216Thr | p.I216T | Q08499 | protein_coding | tolerated_low_confidence(0.29) | possibly_damaging(0.84) | TCGA-A8-A09C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PDE4D | SNV | Missense_Mutation | | c.1895N>A | p.Arg632His | p.R632H | Q08499 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.985) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PDE4D | SNV | Missense_Mutation | | c.1904N>T | p.Thr635Met | p.T635M | Q08499 | protein_coding | deleterious_low_confidence(0) | probably_damaging(1) | TCGA-AN-A0AJ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PDE4D | SNV | Missense_Mutation | | c.896N>A | p.Ser299Tyr | p.S299Y | Q08499 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.974) | TCGA-BH-A0BP-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PDE4D | SNV | Missense_Mutation | | c.1691N>G | p.Lys564Arg | p.K564R | Q08499 | protein_coding | tolerated_low_confidence(0.27) | probably_damaging(0.97) | TCGA-BH-A18T-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
PDE4D | SNV | Missense_Mutation | | c.1291N>T | p.Arg431Trp | p.R431W | Q08499 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.994) | TCGA-C8-A1HL-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
PDE4D | SNV | Missense_Mutation | | c.2221G>C | p.Glu741Gln | p.E741Q | Q08499 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.954) | TCGA-E2-A159-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cyclophosphamide | SD |
PDE4D | insertion | Nonsense_Mutation | novel | c.1924_1925insGTTGTTGTTGAAAATAGTGACAATTTTACCAAACTAAGTTTAG | p.Phe642CysfsTer4 | p.F642Cfs*4 | Q08499 | protein_coding | | | TCGA-A2-A0D1-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | taxotere | SD |
PDE4D | deletion | Frame_Shift_Del | novel | c.2148delN | p.Ser717LeufsTer22 | p.S717Lfs*22 | Q08499 | protein_coding | | | TCGA-EW-A2FV-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | docetaxel | SD |
PDE4D | SNV | Missense_Mutation | novel | c.359N>T | p.Ala120Val | p.A120V | Q08499 | protein_coding | tolerated_low_confidence(0.24) | benign(0.058) | TCGA-VS-A8EH-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR |