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/ASL_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/ASL_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/ASL_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/ASL_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/ASL_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/ASL_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/ASL_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
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/ASL_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:00329707 | Liver | NAFLD | regulation of actin filament-based process | 66/1882 | 397/18723 | 2.92e-05 | 7.72e-04 | 66 |
GO:00482604 | Liver | NAFLD | positive regulation of receptor-mediated endocytosis | 16/1882 | 52/18723 | 3.13e-05 | 8.20e-04 | 16 |
GO:19029057 | Liver | NAFLD | positive regulation of supramolecular fiber organization | 40/1882 | 209/18723 | 4.88e-05 | 1.15e-03 | 40 |
GO:0019627 | Liver | NAFLD | urea metabolic process | 7/1882 | 12/18723 | 5.15e-05 | 1.19e-03 | 7 |
GO:0071941 | Liver | NAFLD | nitrogen cycle metabolic process | 7/1882 | 12/18723 | 5.15e-05 | 1.19e-03 | 7 |
GO:00329567 | Liver | NAFLD | regulation of actin cytoskeleton organization | 60/1882 | 358/18723 | 5.20e-05 | 1.20e-03 | 60 |
GO:01100537 | Liver | NAFLD | regulation of actin filament organization | 49/1882 | 278/18723 | 6.88e-05 | 1.46e-03 | 49 |
GO:00069007 | Liver | NAFLD | vesicle budding from membrane | 17/1882 | 61/18723 | 7.31e-05 | 1.52e-03 | 17 |
GO:2000601 | Liver | NAFLD | positive regulation of Arp2/3 complex-mediated actin nucleation | 6/1882 | 10/18723 | 1.50e-04 | 2.78e-03 | 6 |
GO:00163585 | Liver | NAFLD | dendrite development | 43/1882 | 243/18723 | 1.70e-04 | 3.07e-03 | 43 |
GO:00313465 | Liver | NAFLD | positive regulation of cell projection organization | 57/1882 | 353/18723 | 2.19e-04 | 3.73e-03 | 57 |
GO:00160505 | Liver | NAFLD | vesicle organization | 50/1882 | 300/18723 | 2.42e-04 | 4.06e-03 | 50 |
GO:00488133 | Liver | NAFLD | dendrite morphogenesis | 29/1882 | 146/18723 | 2.63e-04 | 4.26e-03 | 29 |
GO:00432547 | Liver | NAFLD | regulation of protein-containing complex assembly | 66/1882 | 428/18723 | 2.83e-04 | 4.53e-03 | 66 |
GO:00512587 | Liver | NAFLD | protein polymerization | 49/1882 | 297/18723 | 3.54e-04 | 5.36e-03 | 49 |
GO:00482594 | Liver | NAFLD | regulation of receptor-mediated endocytosis | 23/1882 | 110/18723 | 5.16e-04 | 7.15e-03 | 23 |
GO:00725834 | Liver | NAFLD | clathrin-dependent endocytosis | 13/1882 | 47/18723 | 5.46e-04 | 7.45e-03 | 13 |
GO:00343153 | Liver | NAFLD | regulation of Arp2/3 complex-mediated actin nucleation | 8/1882 | 21/18723 | 6.29e-04 | 8.21e-03 | 8 |
GO:00609963 | Liver | NAFLD | dendritic spine development | 21/1882 | 99/18723 | 7.26e-04 | 9.27e-03 | 21 |
GO:00000501 | Liver | NAFLD | urea cycle | 5/1882 | 10/18723 | 1.67e-03 | 1.74e-02 | 5 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa01230 | Colorectum | AD | Biosynthesis of amino acids | 28/2092 | 75/8465 | 9.99e-03 | 3.89e-02 | 2.48e-02 | 28 |
hsa012301 | Colorectum | AD | Biosynthesis of amino acids | 28/2092 | 75/8465 | 9.99e-03 | 3.89e-02 | 2.48e-02 | 28 |
hsa012302 | Colorectum | SER | Biosynthesis of amino acids | 23/1580 | 75/8465 | 8.11e-03 | 4.14e-02 | 3.01e-02 | 23 |
hsa012303 | Colorectum | SER | Biosynthesis of amino acids | 23/1580 | 75/8465 | 8.11e-03 | 4.14e-02 | 3.01e-02 | 23 |
hsa0123023 | Esophagus | ESCC | Biosynthesis of amino acids | 49/4205 | 75/8465 | 4.35e-03 | 1.12e-02 | 5.74e-03 | 49 |
hsa0123033 | Esophagus | ESCC | Biosynthesis of amino acids | 49/4205 | 75/8465 | 4.35e-03 | 1.12e-02 | 5.74e-03 | 49 |
hsa012304 | Liver | Cirrhotic | Biosynthesis of amino acids | 35/2530 | 75/8465 | 1.54e-03 | 7.83e-03 | 4.83e-03 | 35 |
hsa0123011 | Liver | Cirrhotic | Biosynthesis of amino acids | 35/2530 | 75/8465 | 1.54e-03 | 7.83e-03 | 4.83e-03 | 35 |
hsa0123021 | Liver | HCC | Biosynthesis of amino acids | 53/4020 | 75/8465 | 3.79e-05 | 2.11e-04 | 1.18e-04 | 53 |
hsa0123031 | Liver | HCC | Biosynthesis of amino acids | 53/4020 | 75/8465 | 3.79e-05 | 2.11e-04 | 1.18e-04 | 53 |
hsa012305 | Oral cavity | OSCC | Biosynthesis of amino acids | 45/3704 | 75/8465 | 3.27e-03 | 8.23e-03 | 4.19e-03 | 45 |
hsa0123012 | Oral cavity | OSCC | Biosynthesis of amino acids | 45/3704 | 75/8465 | 3.27e-03 | 8.23e-03 | 4.19e-03 | 45 |
hsa00220 | Stomach | GC | Arginine biosynthesis | 6/708 | 22/8465 | 7.81e-03 | 4.10e-02 | 2.88e-02 | 6 |
hsa002201 | Stomach | GC | Arginine biosynthesis | 6/708 | 22/8465 | 7.81e-03 | 4.10e-02 | 2.88e-02 | 6 |
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 |
ASL | SNV | Missense_Mutation | | c.22N>T | p.Leu8Phe | p.L8F | P04424 | protein_coding | deleterious(0) | probably_damaging(0.912) | TCGA-A1-A0SH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tc | SD |
ASL | SNV | Missense_Mutation | | c.1188N>G | p.Phe396Leu | p.F396L | P04424 | protein_coding | tolerated(0.69) | benign(0.003) | TCGA-A8-A09G-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
ASL | SNV | Missense_Mutation | | c.653C>T | p.Ala218Val | p.A218V | P04424 | protein_coding | tolerated(0.08) | benign(0.01) | TCGA-D8-A1XW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin+cyclophosphamide | SD |
ASL | SNV | Missense_Mutation | | c.219N>C | p.Glu73Asp | p.E73D | P04424 | protein_coding | deleterious(0.04) | probably_damaging(1) | TCGA-E2-A14R-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | PD |
ASL | SNV | Missense_Mutation | | c.491N>T | p.Ala164Val | p.A164V | P04424 | protein_coding | deleterious(0) | probably_damaging(0.971) | TCGA-E2-A15M-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD |
ASL | SNV | Missense_Mutation | | c.1188N>G | p.Phe396Leu | p.F396L | P04424 | protein_coding | tolerated(0.69) | benign(0.003) | TCGA-XX-A89A-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
ASL | insertion | Frame_Shift_Ins | novel | c.1285_1286insAA | p.Asp429GlufsTer120 | p.D429Efs*120 | P04424 | protein_coding | | | TCGA-A8-A06P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | | SD |
ASL | insertion | In_Frame_Ins | novel | c.1287_1288insATAAAGGCCAGTAAAACA | p.Asp429_Tyr430insIleLysAlaSerLysThr | p.D429_Y430insIKASKT | P04424 | protein_coding | | | TCGA-A8-A06P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | | SD |
ASL | SNV | Missense_Mutation | novel | c.486N>C | p.Gln162His | p.Q162H | P04424 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-JW-A5VL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
ASL | SNV | Missense_Mutation | | c.535G>A | p.Ala179Thr | p.A179T | P04424 | protein_coding | tolerated(0.13) | possibly_damaging(0.886) | TCGA-AA-3492-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |