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/PLD1_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/PLD1_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/PLD1_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal 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/PLD1_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
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/PLD1_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/PLD1_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00300333 | Colorectum | FAP | microvillus assembly | 7/2622 | 16/18723 | 3.75e-03 | 2.66e-02 | 7 |
GO:0046474 | Colorectum | FAP | glycerophospholipid biosynthetic process | 44/2622 | 211/18723 | 3.98e-03 | 2.76e-02 | 44 |
GO:01200323 | Colorectum | FAP | regulation of plasma membrane bounded cell projection assembly | 39/2622 | 186/18723 | 5.84e-03 | 3.73e-02 | 39 |
GO:00450172 | Colorectum | FAP | glycerolipid biosynthetic process | 50/2622 | 252/18723 | 6.32e-03 | 3.95e-02 | 50 |
GO:00604912 | Colorectum | FAP | regulation of cell projection assembly | 39/2622 | 188/18723 | 7.01e-03 | 4.29e-02 | 39 |
GO:00072653 | Colorectum | CRC | Ras protein signal transduction | 70/2078 | 337/18723 | 1.49e-07 | 1.66e-05 | 70 |
GO:00990033 | Colorectum | CRC | vesicle-mediated transport in synapse | 45/2078 | 200/18723 | 2.67e-06 | 1.25e-04 | 45 |
GO:00064175 | Colorectum | CRC | regulation of translation | 82/2078 | 468/18723 | 1.79e-05 | 5.40e-04 | 82 |
GO:00995042 | Colorectum | CRC | synaptic vesicle cycle | 39/2078 | 181/18723 | 3.43e-05 | 8.71e-04 | 39 |
GO:00086541 | Colorectum | CRC | phospholipid biosynthetic process | 49/2078 | 253/18723 | 7.07e-05 | 1.51e-03 | 49 |
GO:00325284 | Colorectum | CRC | microvillus organization | 10/2078 | 24/18723 | 1.25e-04 | 2.42e-03 | 10 |
GO:00325304 | Colorectum | CRC | regulation of microvillus organization | 7/2078 | 13/18723 | 1.92e-04 | 3.30e-03 | 7 |
GO:00066503 | Colorectum | CRC | glycerophospholipid metabolic process | 55/2078 | 306/18723 | 2.10e-04 | 3.55e-03 | 55 |
GO:00450173 | Colorectum | CRC | glycerolipid biosynthetic process | 47/2078 | 252/18723 | 2.47e-04 | 4.06e-03 | 47 |
GO:00066443 | Colorectum | CRC | phospholipid metabolic process | 65/2078 | 383/18723 | 3.21e-04 | 4.95e-03 | 65 |
GO:00464741 | Colorectum | CRC | glycerophospholipid biosynthetic process | 40/2078 | 211/18723 | 4.91e-04 | 7.02e-03 | 40 |
GO:00300334 | Colorectum | CRC | microvillus assembly | 7/2078 | 16/18723 | 9.47e-04 | 1.15e-02 | 7 |
GO:00464861 | Colorectum | CRC | glycerolipid metabolic process | 64/2078 | 392/18723 | 1.01e-03 | 1.19e-02 | 64 |
GO:01200324 | Colorectum | CRC | regulation of plasma membrane bounded cell projection assembly | 35/2078 | 186/18723 | 1.22e-03 | 1.38e-02 | 35 |
GO:00604913 | Colorectum | CRC | regulation of cell projection assembly | 35/2078 | 188/18723 | 1.48e-03 | 1.58e-02 | 35 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0520820 | Cervix | CC | Chemical carcinogenesis - reactive oxygen species | 92/1267 | 223/8465 | 4.71e-22 | 5.09e-20 | 3.01e-20 | 92 |
hsa0414418 | Cervix | CC | Endocytosis | 64/1267 | 251/8465 | 6.97e-06 | 6.10e-05 | 3.61e-05 | 64 |
hsa0466612 | Cervix | CC | Fc gamma R-mediated phagocytosis | 31/1267 | 97/8465 | 1.78e-05 | 1.42e-04 | 8.40e-05 | 31 |
hsa0407110 | Cervix | CC | Sphingolipid signaling pathway | 35/1267 | 121/8465 | 5.70e-05 | 3.93e-04 | 2.32e-04 | 35 |
hsa052128 | Cervix | CC | Pancreatic cancer | 24/1267 | 76/8465 | 1.89e-04 | 1.11e-03 | 6.55e-04 | 24 |
hsa0491212 | Cervix | CC | GnRH signaling pathway | 26/1267 | 93/8465 | 8.72e-04 | 3.87e-03 | 2.29e-03 | 26 |
hsa0492812 | Cervix | CC | Parathyroid hormone synthesis, secretion and action | 27/1267 | 106/8465 | 3.12e-03 | 1.19e-02 | 7.03e-03 | 27 |
hsa040142 | Cervix | CC | Ras signaling pathway | 51/1267 | 236/8465 | 3.55e-03 | 1.34e-02 | 7.91e-03 | 51 |
hsa05208110 | Cervix | CC | Chemical carcinogenesis - reactive oxygen species | 92/1267 | 223/8465 | 4.71e-22 | 5.09e-20 | 3.01e-20 | 92 |
hsa0414419 | Cervix | CC | Endocytosis | 64/1267 | 251/8465 | 6.97e-06 | 6.10e-05 | 3.61e-05 | 64 |
hsa0466613 | Cervix | CC | Fc gamma R-mediated phagocytosis | 31/1267 | 97/8465 | 1.78e-05 | 1.42e-04 | 8.40e-05 | 31 |
hsa0407113 | Cervix | CC | Sphingolipid signaling pathway | 35/1267 | 121/8465 | 5.70e-05 | 3.93e-04 | 2.32e-04 | 35 |
hsa0521213 | Cervix | CC | Pancreatic cancer | 24/1267 | 76/8465 | 1.89e-04 | 1.11e-03 | 6.55e-04 | 24 |
hsa0491213 | Cervix | CC | GnRH signaling pathway | 26/1267 | 93/8465 | 8.72e-04 | 3.87e-03 | 2.29e-03 | 26 |
hsa0492813 | Cervix | CC | Parathyroid hormone synthesis, secretion and action | 27/1267 | 106/8465 | 3.12e-03 | 1.19e-02 | 7.03e-03 | 27 |
hsa0401411 | Cervix | CC | Ras signaling pathway | 51/1267 | 236/8465 | 3.55e-03 | 1.34e-02 | 7.91e-03 | 51 |
hsa05208 | Colorectum | AD | Chemical carcinogenesis - reactive oxygen species | 126/2092 | 223/8465 | 1.01e-24 | 1.68e-22 | 1.07e-22 | 126 |
hsa04144 | Colorectum | AD | Endocytosis | 111/2092 | 251/8465 | 5.95e-12 | 1.42e-10 | 9.08e-11 | 111 |
hsa04666 | Colorectum | AD | Fc gamma R-mediated phagocytosis | 46/2092 | 97/8465 | 9.10e-07 | 1.22e-05 | 7.77e-06 | 46 |
hsa04912 | Colorectum | AD | GnRH signaling pathway | 35/2092 | 93/8465 | 3.69e-03 | 1.90e-02 | 1.21e-02 | 35 |
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 |
PLD1 | SNV | Missense_Mutation | rs774453063 | c.1376N>G | p.Tyr459Cys | p.Y459C | Q13393 | protein_coding | deleterious(0) | probably_damaging(0.981) | TCGA-A2-A25D-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | tamoxiphen | SD |
PLD1 | SNV | Missense_Mutation | | c.1448N>T | p.Ala483Val | p.A483V | Q13393 | protein_coding | deleterious(0.01) | probably_damaging(0.995) | TCGA-A8-A08P-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | 5-fluorouracil | CR |
PLD1 | SNV | Missense_Mutation | | c.1583N>C | p.Lys528Thr | p.K528T | Q13393 | protein_coding | tolerated(0.46) | benign(0.013) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PLD1 | SNV | Missense_Mutation | | c.734G>A | p.Arg245Lys | p.R245K | Q13393 | protein_coding | tolerated(0.52) | benign(0.021) | TCGA-AR-A0TX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PLD1 | SNV | Missense_Mutation | | c.1183G>C | p.Glu395Gln | p.E395Q | Q13393 | protein_coding | tolerated(0.05) | possibly_damaging(0.84) | TCGA-C8-A1HK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PLD1 | SNV | Missense_Mutation | | c.3218N>C | p.Trp1073Ser | p.W1073S | Q13393 | protein_coding | deleterious(0) | probably_damaging(0.99) | TCGA-C8-A27B-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
PLD1 | SNV | Missense_Mutation | | c.247G>A | p.Ala83Thr | p.A83T | Q13393 | protein_coding | deleterious(0.04) | benign(0.287) | TCGA-D8-A27N-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | taxol+adriamycin+cyclophosphamide+herceptin | SD |
PLD1 | SNV | Missense_Mutation | novel | c.179C>A | p.Ala60Asp | p.A60D | Q13393 | protein_coding | tolerated(0.06) | benign(0.282) | TCGA-MS-A51U-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
PLD1 | deletion | Frame_Shift_Del | novel | c.2769_2770delNN | p.Asp924GlnfsTer2 | p.D924Qfs*2 | Q13393 | protein_coding | | | TCGA-A2-A3XY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | PD |
PLD1 | insertion | Frame_Shift_Ins | novel | c.75_76insCGTCTCACCCCTGCCAATTGCCTGGTGCACGGCTTATATTTGTG | p.Glu26ArgfsTer30 | p.E26Rfs*30 | Q13393 | protein_coding | | | TCGA-AO-A0J9-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | PD |