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:00457272 | Colorectum | MSS | positive regulation of translation | 43/3467 | 136/18723 | 1.60e-04 | 2.29e-03 | 43 |
GO:00300332 | Colorectum | MSS | microvillus assembly | 9/3467 | 16/18723 | 8.20e-04 | 8.59e-03 | 9 |
GO:01200322 | Colorectum | MSS | regulation of plasma membrane bounded cell projection assembly | 51/3467 | 186/18723 | 1.78e-03 | 1.58e-02 | 51 |
GO:00990031 | Colorectum | MSS | vesicle-mediated transport in synapse | 54/3467 | 200/18723 | 1.94e-03 | 1.67e-02 | 54 |
GO:00604911 | Colorectum | MSS | regulation of cell projection assembly | 51/3467 | 188/18723 | 2.28e-03 | 1.87e-02 | 51 |
GO:0099504 | Colorectum | MSS | synaptic vesicle cycle | 48/3467 | 181/18723 | 4.85e-03 | 3.39e-02 | 48 |
GO:00160422 | Colorectum | MSS | lipid catabolic process | 77/3467 | 320/18723 | 7.43e-03 | 4.71e-02 | 77 |
GO:00064174 | Colorectum | FAP | regulation of translation | 111/2622 | 468/18723 | 8.47e-09 | 1.13e-06 | 111 |
GO:00072652 | Colorectum | FAP | Ras protein signal transduction | 80/2622 | 337/18723 | 9.61e-07 | 4.33e-05 | 80 |
GO:00990032 | Colorectum | FAP | vesicle-mediated transport in synapse | 51/2622 | 200/18723 | 1.09e-05 | 3.08e-04 | 51 |
GO:00995041 | Colorectum | FAP | synaptic vesicle cycle | 45/2622 | 181/18723 | 6.73e-05 | 1.28e-03 | 45 |
GO:00325303 | Colorectum | FAP | regulation of microvillus organization | 8/2622 | 13/18723 | 9.75e-05 | 1.65e-03 | 8 |
GO:00325283 | Colorectum | FAP | microvillus organization | 11/2622 | 24/18723 | 1.70e-04 | 2.56e-03 | 11 |
GO:00342504 | Colorectum | FAP | positive regulation of cellular amide metabolic process | 39/2622 | 162/18723 | 4.02e-04 | 4.86e-03 | 39 |
GO:00457274 | Colorectum | FAP | positive regulation of translation | 34/2622 | 136/18723 | 4.43e-04 | 5.25e-03 | 34 |
GO:0008654 | Colorectum | FAP | phospholipid biosynthetic process | 54/2622 | 253/18723 | 8.88e-04 | 9.08e-03 | 54 |
GO:00160423 | Colorectum | FAP | lipid catabolic process | 65/2622 | 320/18723 | 1.13e-03 | 1.08e-02 | 65 |
GO:00066502 | Colorectum | FAP | glycerophospholipid metabolic process | 62/2622 | 306/18723 | 1.54e-03 | 1.38e-02 | 62 |
GO:00066442 | Colorectum | FAP | phospholipid metabolic process | 74/2622 | 383/18723 | 2.24e-03 | 1.83e-02 | 74 |
GO:0046473 | Colorectum | FAP | phosphatidic acid metabolic process | 12/2622 | 37/18723 | 3.43e-03 | 2.48e-02 | 12 |
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 |