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/PCK1_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/PCK1_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
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/PCK1_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/PCK1_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00319605 | Stomach | SIM | response to corticosteroid | 22/708 | 167/18723 | 3.52e-07 | 2.37e-05 | 22 |
GO:00224075 | Stomach | SIM | regulation of cell-cell adhesion | 40/708 | 448/18723 | 4.73e-07 | 3.05e-05 | 40 |
GO:00324965 | Stomach | SIM | response to lipopolysaccharide | 33/708 | 343/18723 | 9.30e-07 | 5.42e-05 | 33 |
GO:00066411 | Stomach | SIM | triglyceride metabolic process | 16/708 | 100/18723 | 1.03e-06 | 5.84e-05 | 16 |
GO:00316675 | Stomach | SIM | response to nutrient levels | 40/708 | 474/18723 | 1.97e-06 | 1.02e-04 | 40 |
GO:00713565 | Stomach | SIM | cellular response to tumor necrosis factor | 25/708 | 229/18723 | 2.06e-06 | 1.05e-04 | 25 |
GO:00508705 | Stomach | SIM | positive regulation of T cell activation | 24/708 | 216/18723 | 2.41e-06 | 1.18e-04 | 24 |
GO:00513845 | Stomach | SIM | response to glucocorticoid | 19/708 | 148/18723 | 3.24e-06 | 1.54e-04 | 19 |
GO:00224095 | Stomach | SIM | positive regulation of cell-cell adhesion | 28/708 | 284/18723 | 3.86e-06 | 1.68e-04 | 28 |
GO:00346125 | Stomach | SIM | response to tumor necrosis factor | 26/708 | 253/18723 | 4.00e-06 | 1.70e-04 | 26 |
GO:19030395 | Stomach | SIM | positive regulation of leukocyte cell-cell adhesion | 25/708 | 239/18723 | 4.46e-06 | 1.88e-04 | 25 |
GO:19030375 | Stomach | SIM | regulation of leukocyte cell-cell adhesion | 31/708 | 336/18723 | 4.73e-06 | 1.94e-04 | 31 |
GO:00071595 | Stomach | SIM | leukocyte cell-cell adhesion | 33/708 | 371/18723 | 5.16e-06 | 2.08e-04 | 33 |
GO:004854551 | Stomach | SIM | response to steroid hormone | 31/708 | 339/18723 | 5.67e-06 | 2.25e-04 | 31 |
GO:00466835 | Stomach | SIM | response to organophosphorus | 17/708 | 131/18723 | 9.13e-06 | 3.39e-04 | 17 |
GO:00515915 | Stomach | SIM | response to cAMP | 14/708 | 93/18723 | 1.00e-05 | 3.67e-04 | 14 |
GO:000974351 | Stomach | SIM | response to carbohydrate | 25/708 | 253/18723 | 1.21e-05 | 4.30e-04 | 25 |
GO:19016545 | Stomach | SIM | response to ketone | 21/708 | 194/18723 | 1.52e-05 | 5.11e-04 | 21 |
GO:003428451 | Stomach | SIM | response to monosaccharide | 23/708 | 225/18723 | 1.55e-05 | 5.19e-04 | 23 |
GO:00508635 | Stomach | SIM | regulation of T cell activation | 29/708 | 329/18723 | 2.26e-05 | 7.00e-04 | 29 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa00620 | Colorectum | AD | Pyruvate metabolism | 28/2092 | 47/8465 | 3.71e-07 | 5.41e-06 | 3.45e-06 | 28 |
hsa00020 | Colorectum | AD | Citrate cycle (TCA cycle) | 20/2092 | 30/8465 | 1.43e-06 | 1.77e-05 | 1.13e-05 | 20 |
hsa00010 | Colorectum | AD | Glycolysis / Gluconeogenesis | 34/2092 | 67/8465 | 3.63e-06 | 4.34e-05 | 2.77e-05 | 34 |
hsa04152 | Colorectum | AD | AMPK signaling pathway | 47/2092 | 121/8465 | 3.74e-04 | 2.82e-03 | 1.80e-03 | 47 |
hsa04922 | Colorectum | AD | Glucagon signaling pathway | 41/2092 | 107/8465 | 1.18e-03 | 7.75e-03 | 4.94e-03 | 41 |
hsa04964 | Colorectum | AD | Proximal tubule bicarbonate reclamation | 11/2092 | 23/8465 | 1.35e-02 | 4.86e-02 | 3.10e-02 | 11 |
hsa006201 | Colorectum | AD | Pyruvate metabolism | 28/2092 | 47/8465 | 3.71e-07 | 5.41e-06 | 3.45e-06 | 28 |
hsa000201 | Colorectum | AD | Citrate cycle (TCA cycle) | 20/2092 | 30/8465 | 1.43e-06 | 1.77e-05 | 1.13e-05 | 20 |
hsa000101 | Colorectum | AD | Glycolysis / Gluconeogenesis | 34/2092 | 67/8465 | 3.63e-06 | 4.34e-05 | 2.77e-05 | 34 |
hsa041521 | Colorectum | AD | AMPK signaling pathway | 47/2092 | 121/8465 | 3.74e-04 | 2.82e-03 | 1.80e-03 | 47 |
hsa049221 | Colorectum | AD | Glucagon signaling pathway | 41/2092 | 107/8465 | 1.18e-03 | 7.75e-03 | 4.94e-03 | 41 |
hsa049641 | Colorectum | AD | Proximal tubule bicarbonate reclamation | 11/2092 | 23/8465 | 1.35e-02 | 4.86e-02 | 3.10e-02 | 11 |
hsa006202 | Colorectum | SER | Pyruvate metabolism | 22/1580 | 47/8465 | 9.62e-06 | 1.33e-04 | 9.67e-05 | 22 |
hsa000202 | Colorectum | SER | Citrate cycle (TCA cycle) | 16/1580 | 30/8465 | 2.06e-05 | 2.74e-04 | 1.99e-04 | 16 |
hsa049222 | Colorectum | SER | Glucagon signaling pathway | 38/1580 | 107/8465 | 2.57e-05 | 3.28e-04 | 2.38e-04 | 38 |
hsa000102 | Colorectum | SER | Glycolysis / Gluconeogenesis | 24/1580 | 67/8465 | 6.62e-04 | 5.36e-03 | 3.89e-03 | 24 |
hsa049642 | Colorectum | SER | Proximal tubule bicarbonate reclamation | 10/1580 | 23/8465 | 5.33e-03 | 3.28e-02 | 2.38e-02 | 10 |
hsa006203 | Colorectum | SER | Pyruvate metabolism | 22/1580 | 47/8465 | 9.62e-06 | 1.33e-04 | 9.67e-05 | 22 |
hsa000203 | Colorectum | SER | Citrate cycle (TCA cycle) | 16/1580 | 30/8465 | 2.06e-05 | 2.74e-04 | 1.99e-04 | 16 |
hsa049223 | Colorectum | SER | Glucagon signaling pathway | 38/1580 | 107/8465 | 2.57e-05 | 3.28e-04 | 2.38e-04 | 38 |
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 |
PCK1 | SNV | Missense_Mutation | novel | c.85N>A | p.Glu29Lys | p.E29K | P35558 | protein_coding | tolerated(0.59) | benign(0.003) | TCGA-A7-A4SA-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | CR |
PCK1 | SNV | Missense_Mutation | | c.689C>G | p.Ser230Cys | p.S230C | P35558 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
PCK1 | SNV | Missense_Mutation | | c.521N>G | p.Thr174Arg | p.T174R | P35558 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AC-A6IX-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
PCK1 | SNV | Missense_Mutation | novel | c.369N>T | p.Glu123Asp | p.E123D | P35558 | protein_coding | tolerated(0.57) | benign(0) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PCK1 | SNV | Missense_Mutation | novel | c.1779N>T | p.Glu593Asp | p.E593D | P35558 | protein_coding | tolerated(0.08) | benign(0) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PCK1 | SNV | Missense_Mutation | | c.650C>A | p.Thr217Lys | p.T217K | P35558 | protein_coding | tolerated(0.87) | benign(0.213) | TCGA-AO-A0JD-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cyclophosphamide | SD |
PCK1 | SNV | Missense_Mutation | | c.584N>T | p.Ser195Phe | p.S195F | P35558 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-B6-A1KF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
PCK1 | SNV | Missense_Mutation | | c.1180N>C | p.Glu394Gln | p.E394Q | P35558 | protein_coding | tolerated(0.26) | benign(0.019) | TCGA-BH-A0HK-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
PCK1 | SNV | Missense_Mutation | novel | c.715T>C | p.Ser239Pro | p.S239P | P35558 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-C8-A1HG-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
PCK1 | SNV | Missense_Mutation | novel | c.971N>T | p.Arg324Met | p.R324M | P35558 | protein_coding | tolerated(0.05) | possibly_damaging(0.904) | TCGA-OL-A97C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |