Tissue | Expression Dynamics | Abbreviation |
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/C2_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/C2_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
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/C2_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
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/C2_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:001032421 | Cervix | N_HPV | membrane invagination | 15/534 | 144/18723 | 1.60e-05 | 4.86e-04 | 15 |
GO:00069111 | Cervix | N_HPV | phagocytosis, engulfment | 14/534 | 127/18723 | 1.61e-05 | 4.86e-04 | 14 |
GO:001046623 | Cervix | N_HPV | negative regulation of peptidase activity | 21/534 | 262/18723 | 2.18e-05 | 6.16e-04 | 21 |
GO:00509202 | Cervix | N_HPV | regulation of chemotaxis | 19/534 | 223/18723 | 2.29e-05 | 6.37e-04 | 19 |
GO:000701525 | Cervix | N_HPV | actin filament organization | 29/534 | 442/18723 | 3.00e-05 | 8.02e-04 | 29 |
GO:003297025 | Cervix | N_HPV | regulation of actin filament-based process | 27/534 | 397/18723 | 3.03e-05 | 8.02e-04 | 27 |
GO:000225321 | Cervix | N_HPV | activation of immune response | 26/534 | 375/18723 | 3.06e-05 | 8.02e-04 | 26 |
GO:000675424 | Cervix | N_HPV | ATP biosynthetic process | 9/534 | 57/18723 | 3.10e-05 | 8.03e-04 | 9 |
GO:00990241 | Cervix | N_HPV | plasma membrane invagination | 14/534 | 136/18723 | 3.49e-05 | 8.79e-04 | 14 |
GO:007265514 | Cervix | N_HPV | establishment of protein localization to mitochondrion | 13/534 | 120/18723 | 3.86e-05 | 9.41e-04 | 13 |
GO:00026972 | Cervix | N_HPV | regulation of immune effector process | 24/534 | 339/18723 | 4.42e-05 | 1.04e-03 | 24 |
GO:001598524 | Cervix | N_HPV | energy coupled proton transport, down electrochemical gradient | 6/534 | 26/18723 | 7.41e-05 | 1.59e-03 | 6 |
GO:001598624 | Cervix | N_HPV | ATP synthesis coupled proton transport | 6/534 | 26/18723 | 7.41e-05 | 1.59e-03 | 6 |
GO:000695611 | Cervix | N_HPV | complement activation | 13/534 | 130/18723 | 8.91e-05 | 1.86e-03 | 13 |
GO:007162221 | Cervix | N_HPV | regulation of granulocyte chemotaxis | 8/534 | 51/18723 | 8.99e-05 | 1.86e-03 | 8 |
GO:0002703 | Cervix | N_HPV | regulation of leukocyte mediated immunity | 18/534 | 226/18723 | 9.00e-05 | 1.86e-03 | 18 |
GO:009890112 | Cervix | N_HPV | regulation of cardiac muscle cell action potential | 6/534 | 27/18723 | 9.30e-05 | 1.91e-03 | 6 |
GO:005134624 | Cervix | N_HPV | negative regulation of hydrolase activity | 25/534 | 379/18723 | 9.66e-05 | 1.97e-03 | 25 |
GO:00027682 | Cervix | N_HPV | immune response-regulating cell surface receptor signaling pathway | 22/534 | 315/18723 | 1.11e-04 | 2.18e-03 | 22 |
GO:000920524 | Cervix | N_HPV | purine ribonucleoside triphosphate metabolic process | 10/534 | 82/18723 | 1.11e-04 | 2.18e-03 | 10 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa051714 | Colorectum | MSS | Coronavirus disease - COVID-19 | 108/1875 | 232/8465 | 6.50e-17 | 1.67e-15 | 1.03e-15 | 108 |
hsa051715 | Colorectum | MSS | Coronavirus disease - COVID-19 | 108/1875 | 232/8465 | 6.50e-17 | 1.67e-15 | 1.03e-15 | 108 |
hsa051716 | Colorectum | MSI-H | Coronavirus disease - COVID-19 | 91/797 | 232/8465 | 2.21e-35 | 3.58e-33 | 3.00e-33 | 91 |
hsa051717 | Colorectum | MSI-H | Coronavirus disease - COVID-19 | 91/797 | 232/8465 | 2.21e-35 | 3.58e-33 | 3.00e-33 | 91 |
hsa0517122 | Liver | Cirrhotic | Coronavirus disease - COVID-19 | 136/2530 | 232/8465 | 3.28e-20 | 1.82e-18 | 1.12e-18 | 136 |
hsa046102 | Liver | Cirrhotic | Complement and coagulation cascades | 48/2530 | 86/8465 | 4.41e-07 | 5.44e-06 | 3.35e-06 | 48 |
hsa05133 | Liver | Cirrhotic | Pertussis | 37/2530 | 76/8465 | 4.17e-04 | 2.57e-03 | 1.58e-03 | 37 |
hsa04936 | Liver | Cirrhotic | Alcoholic liver disease | 60/2530 | 142/8465 | 1.07e-03 | 5.85e-03 | 3.61e-03 | 60 |
hsa0517132 | Liver | Cirrhotic | Coronavirus disease - COVID-19 | 136/2530 | 232/8465 | 3.28e-20 | 1.82e-18 | 1.12e-18 | 136 |
hsa046103 | Liver | Cirrhotic | Complement and coagulation cascades | 48/2530 | 86/8465 | 4.41e-07 | 5.44e-06 | 3.35e-06 | 48 |
hsa051331 | Liver | Cirrhotic | Pertussis | 37/2530 | 76/8465 | 4.17e-04 | 2.57e-03 | 1.58e-03 | 37 |
hsa049361 | Liver | Cirrhotic | Alcoholic liver disease | 60/2530 | 142/8465 | 1.07e-03 | 5.85e-03 | 3.61e-03 | 60 |
hsa0517142 | Liver | HCC | Coronavirus disease - COVID-19 | 167/4020 | 232/8465 | 1.50e-14 | 4.19e-13 | 2.33e-13 | 167 |
hsa049362 | Liver | HCC | Alcoholic liver disease | 89/4020 | 142/8465 | 1.73e-04 | 8.53e-04 | 4.75e-04 | 89 |
hsa046104 | Liver | HCC | Complement and coagulation cascades | 57/4020 | 86/8465 | 3.19e-04 | 1.45e-03 | 8.04e-04 | 57 |
hsa051332 | Liver | HCC | Pertussis | 48/4020 | 76/8465 | 4.17e-03 | 1.27e-02 | 7.06e-03 | 48 |
hsa0517152 | Liver | HCC | Coronavirus disease - COVID-19 | 167/4020 | 232/8465 | 1.50e-14 | 4.19e-13 | 2.33e-13 | 167 |
hsa049363 | Liver | HCC | Alcoholic liver disease | 89/4020 | 142/8465 | 1.73e-04 | 8.53e-04 | 4.75e-04 | 89 |
hsa046105 | Liver | HCC | Complement and coagulation cascades | 57/4020 | 86/8465 | 3.19e-04 | 1.45e-03 | 8.04e-04 | 57 |
hsa051333 | Liver | HCC | Pertussis | 48/4020 | 76/8465 | 4.17e-03 | 1.27e-02 | 7.06e-03 | 48 |
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 |
C2 | SNV | Missense_Mutation | novel | c.1050N>A | p.Met350Ile | p.M350I | P06681 | protein_coding | tolerated(0.19) | possibly_damaging(0.511) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
C2 | SNV | Missense_Mutation | | c.346G>A | p.Glu116Lys | p.E116K | P06681 | protein_coding | tolerated(0.06) | benign(0.215) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
C2 | SNV | Missense_Mutation | novel | c.803N>G | p.Asn268Ser | p.N268S | P06681 | protein_coding | tolerated(0.77) | benign(0) | TCGA-AC-A3QQ-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
C2 | SNV | Missense_Mutation | rs567227615 | c.256N>T | p.Pro86Ser | p.P86S | P06681 | protein_coding | tolerated(0.13) | benign(0.028) | TCGA-BH-A18Q-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
C2 | SNV | Missense_Mutation | rs764034564 | c.185N>A | p.Arg62Gln | p.R62Q | P06681 | protein_coding | deleterious(0.02) | benign(0.366) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
C2 | insertion | Frame_Shift_Ins | novel | c.2056_2057insCATGTCTGGCTAATTTTTGTATTTTT | p.Glu686AlafsTer21 | p.E686Afs*21 | P06681 | protein_coding | | | TCGA-AO-A0JB-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD |
C2 | deletion | Frame_Shift_Del | novel | c.729_739delNNNNNNNNNNN | p.Lys244ProfsTer22 | p.K244Pfs*22 | P06681 | protein_coding | | | TCGA-BH-A1F6-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
C2 | SNV | Missense_Mutation | rs766407308 | c.394C>T | p.Arg132Cys | p.R132C | P06681 | protein_coding | deleterious(0.02) | benign(0.012) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
C2 | SNV | Missense_Mutation | | c.1315N>G | p.Leu439Val | p.L439V | P06681 | protein_coding | tolerated(0.43) | benign(0.26) | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD |
C2 | SNV | Missense_Mutation | | c.811C>G | p.Leu271Val | p.L271V | P06681 | protein_coding | tolerated(0.24) | benign(0) | TCGA-LP-A4AV-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |