Tissue | Expression Dynamics | Abbreviation |
Breast | ![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/Breast/CALM1_pca_on_diff_genes.png) | IDC: Invasive ductal carcinoma |
DCIS: Ductal carcinoma in situ |
Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers |
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/CALM1_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/CALM1_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/CALM1_pca_on_diff_genes.png) | AD: Adenomas |
SER: Sessile serrated lesions |
MSI-H: Microsatellite-high colorectal cancer |
MSS: Microsatellite stable colorectal cancer |
Endometrium | ![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/Endometrium/CALM1_pca_on_diff_genes.png) | AEH: Atypical endometrial hyperplasia |
EEC: Endometrioid 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/CALM1_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
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/CALM1_pca_on_diff_genes.png) | HCC: Hepatocellular carcinoma |
NAFLD: Non-alcoholic fatty liver disease |
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/CALM1_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
Prostate | ![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/Prostate/CALM1_pca_on_diff_genes.png) | BPH: Benign Prostatic Hyperplasia |
Skin | ![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/Skin/CALM1_pca_on_diff_genes.png) | AK: Actinic keratosis |
cSCC: Cutaneous squamous cell carcinoma |
SCCIS:squamous cell carcinoma in situ |
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/CALM1_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:00484881 | Colorectum | CRC | synaptic vesicle endocytosis | 14/2078 | 62/18723 | 7.05e-03 | 4.92e-02 | 14 |
GO:01402381 | Colorectum | CRC | presynaptic endocytosis | 14/2078 | 62/18723 | 7.05e-03 | 4.92e-02 | 14 |
GO:00516514 | Colorectum | CRC | maintenance of location in cell | 36/2078 | 214/18723 | 7.25e-03 | 4.98e-02 | 36 |
GO:004854516 | Endometrium | AEH | response to steroid hormone | 76/2100 | 339/18723 | 2.15e-09 | 1.77e-07 | 76 |
GO:007259410 | Endometrium | AEH | establishment of protein localization to organelle | 89/2100 | 422/18723 | 2.41e-09 | 1.90e-07 | 89 |
GO:005109816 | Endometrium | AEH | regulation of binding | 77/2100 | 363/18723 | 2.21e-08 | 1.31e-06 | 77 |
GO:190165415 | Endometrium | AEH | response to ketone | 45/2100 | 194/18723 | 1.48e-06 | 4.69e-05 | 45 |
GO:005109916 | Endometrium | AEH | positive regulation of binding | 41/2100 | 173/18723 | 2.39e-06 | 6.92e-05 | 41 |
GO:007058510 | Endometrium | AEH | protein localization to mitochondrion | 32/2100 | 125/18723 | 5.38e-06 | 1.36e-04 | 32 |
GO:00009108 | Endometrium | AEH | cytokinesis | 40/2100 | 173/18723 | 6.01e-06 | 1.49e-04 | 40 |
GO:007265510 | Endometrium | AEH | establishment of protein localization to mitochondrion | 31/2100 | 120/18723 | 6.13e-06 | 1.50e-04 | 31 |
GO:002241115 | Endometrium | AEH | cellular component disassembly | 80/2100 | 443/18723 | 1.07e-05 | 2.45e-04 | 80 |
GO:002176215 | Endometrium | AEH | substantia nigra development | 16/2100 | 44/18723 | 1.14e-05 | 2.54e-04 | 16 |
GO:00989019 | Endometrium | AEH | regulation of cardiac muscle cell action potential | 12/2100 | 27/18723 | 1.32e-05 | 2.84e-04 | 12 |
GO:00106495 | Endometrium | AEH | regulation of cell communication by electrical coupling | 9/2100 | 16/18723 | 1.51e-05 | 3.19e-04 | 9 |
GO:00301009 | Endometrium | AEH | regulation of endocytosis | 44/2100 | 211/18723 | 3.39e-05 | 6.05e-04 | 44 |
GO:003196010 | Endometrium | AEH | response to corticosteroid | 37/2100 | 167/18723 | 3.59e-05 | 6.28e-04 | 37 |
GO:009015010 | Endometrium | AEH | establishment of protein localization to membrane | 51/2100 | 260/18723 | 4.74e-05 | 7.85e-04 | 51 |
GO:005165116 | Endometrium | AEH | maintenance of location in cell | 44/2100 | 214/18723 | 4.84e-05 | 7.94e-04 | 44 |
GO:19018447 | Endometrium | AEH | regulation of cell communication by electrical coupling involved in cardiac conduction | 7/2100 | 11/18723 | 4.84e-05 | 7.94e-04 | 7 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501218 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
hsa0501016 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
hsa0502216 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
hsa0516718 | Breast | Precancer | Kaposi sarcoma-associated herpesvirus infection | 36/684 | 194/8465 | 1.68e-06 | 2.53e-05 | 1.94e-05 | 36 |
hsa0491518 | Breast | Precancer | Estrogen signaling pathway | 28/684 | 138/8465 | 4.10e-06 | 5.39e-05 | 4.13e-05 | 28 |
hsa0541818 | Breast | Precancer | Fluid shear stress and atherosclerosis | 28/684 | 139/8465 | 4.74e-06 | 6.00e-05 | 4.59e-05 | 28 |
hsa0541718 | Breast | Precancer | Lipid and atherosclerosis | 37/684 | 215/8465 | 7.64e-06 | 9.29e-05 | 7.12e-05 | 37 |
hsa042189 | Breast | Precancer | Cellular senescence | 29/684 | 156/8465 | 1.66e-05 | 1.69e-04 | 1.30e-04 | 29 |
hsa05031 | Breast | Precancer | Amphetamine addiction | 14/684 | 69/8465 | 1.05e-03 | 7.35e-03 | 5.63e-03 | 14 |
hsa0516316 | Breast | Precancer | Human cytomegalovirus infection | 32/684 | 225/8465 | 1.13e-03 | 7.57e-03 | 5.80e-03 | 32 |
hsa0497114 | Breast | Precancer | Gastric acid secretion | 13/684 | 76/8465 | 7.35e-03 | 4.07e-02 | 3.12e-02 | 13 |
hsa0501219 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
hsa0501017 | Breast | Precancer | Alzheimer disease | 103/684 | 384/8465 | 1.03e-29 | 4.66e-28 | 3.57e-28 | 103 |
hsa0502217 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
hsa0516719 | Breast | Precancer | Kaposi sarcoma-associated herpesvirus infection | 36/684 | 194/8465 | 1.68e-06 | 2.53e-05 | 1.94e-05 | 36 |
hsa0491519 | Breast | Precancer | Estrogen signaling pathway | 28/684 | 138/8465 | 4.10e-06 | 5.39e-05 | 4.13e-05 | 28 |
hsa0541819 | Breast | Precancer | Fluid shear stress and atherosclerosis | 28/684 | 139/8465 | 4.74e-06 | 6.00e-05 | 4.59e-05 | 28 |
hsa0541719 | Breast | Precancer | Lipid and atherosclerosis | 37/684 | 215/8465 | 7.64e-06 | 9.29e-05 | 7.12e-05 | 37 |
hsa0421814 | Breast | Precancer | Cellular senescence | 29/684 | 156/8465 | 1.66e-05 | 1.69e-04 | 1.30e-04 | 29 |
hsa050311 | Breast | Precancer | Amphetamine addiction | 14/684 | 69/8465 | 1.05e-03 | 7.35e-03 | 5.63e-03 | 14 |
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 |
CALM1 | SNV | Missense_Mutation | | c.400N>A | p.Asp134Asn | p.D134N | P62158 | protein_coding | deleterious_low_confidence(0.03) | possibly_damaging(0.574) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
CALM1 | SNV | Missense_Mutation | | c.241N>A | p.Asp81Asn | p.D81N | P62158 | protein_coding | deleterious_low_confidence(0.03) | benign(0.043) | TCGA-C5-A1BQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR |
CALM1 | SNV | Missense_Mutation | | c.202G>A | p.Glu68Lys | p.E68K | P62158 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.932) | TCGA-AA-3977-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
CALM1 | SNV | Missense_Mutation | | c.202N>A | p.Glu68Lys | p.E68K | P62158 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.932) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CALM1 | SNV | Missense_Mutation | novel | c.169N>A | p.Asp57Asn | p.D57N | P62158 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.972) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CALM1 | SNV | Missense_Mutation | | c.210N>T | p.Leu70Phe | p.L70F | P62158 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.67) | TCGA-05-4415-01 | Lung | lung adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | PD |
CALM1 | SNV | Missense_Mutation | novel | c.219N>T | p.Met73Ile | p.M73I | P62158 | protein_coding | deleterious_low_confidence(0.02) | possibly_damaging(0.654) | TCGA-55-7907-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
CALM1 | SNV | Missense_Mutation | novel | c.17N>T | p.Thr6Ile | p.T6I | P62158 | protein_coding | deleterious_low_confidence(0) | benign(0.272) | TCGA-60-2695-01 | Lung | lung squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CALM1 | SNV | Missense_Mutation | novel | c.76N>T | p.Gly26Cys | p.G26C | P62158 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.918) | TCGA-85-8287-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |
CALM1 | SNV | Missense_Mutation | novel | c.77N>T | p.Gly26Val | p.G26V | P62158 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.983) | TCGA-85-8287-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD |