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/CALM3_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/CALM3_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
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/CALM3_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/CALM3_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/CALM3_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/CALM3_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/CALM3_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/CALM3_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/CALM3_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:001056328 | Skin | cSCC | negative regulation of phosphorus metabolic process | 160/4864 | 442/18723 | 1.04e-06 | 1.85e-05 | 160 |
GO:005109927 | Skin | cSCC | positive regulation of binding | 74/4864 | 173/18723 | 1.09e-06 | 1.93e-05 | 74 |
GO:009015119 | Skin | cSCC | establishment of protein localization to mitochondrial membrane | 20/4864 | 30/18723 | 3.41e-06 | 5.20e-05 | 20 |
GO:1901654112 | Skin | cSCC | response to ketone | 79/4864 | 194/18723 | 4.82e-06 | 7.06e-05 | 79 |
GO:004232626 | Skin | cSCC | negative regulation of phosphorylation | 137/4864 | 385/18723 | 1.63e-05 | 1.99e-04 | 137 |
GO:000008611 | Skin | cSCC | G2/M transition of mitotic cell cycle | 58/4864 | 137/18723 | 2.19e-05 | 2.54e-04 | 58 |
GO:000193326 | Skin | cSCC | negative regulation of protein phosphorylation | 123/4864 | 342/18723 | 2.48e-05 | 2.82e-04 | 123 |
GO:001003829 | Skin | cSCC | response to metal ion | 132/4864 | 373/18723 | 3.11e-05 | 3.42e-04 | 132 |
GO:004483911 | Skin | cSCC | cell cycle G2/M phase transition | 61/4864 | 148/18723 | 3.61e-05 | 3.90e-04 | 61 |
GO:0035304112 | Skin | cSCC | regulation of protein dephosphorylation | 41/4864 | 90/18723 | 4.61e-05 | 4.80e-04 | 41 |
GO:004677715 | Skin | cSCC | protein autophosphorylation | 84/4864 | 227/18723 | 1.53e-04 | 1.35e-03 | 84 |
GO:007190024 | Skin | cSCC | regulation of protein serine/threonine kinase activity | 123/4864 | 359/18723 | 2.70e-04 | 2.17e-03 | 123 |
GO:0043388110 | Skin | cSCC | positive regulation of DNA binding | 27/4864 | 56/18723 | 2.84e-04 | 2.27e-03 | 27 |
GO:0051384110 | Skin | cSCC | response to glucocorticoid | 57/4864 | 148/18723 | 5.30e-04 | 3.97e-03 | 57 |
GO:0031960110 | Skin | cSCC | response to corticosteroid | 63/4864 | 167/18723 | 5.35e-04 | 3.97e-03 | 63 |
GO:0035303112 | Skin | cSCC | regulation of dephosphorylation | 49/4864 | 128/18723 | 1.46e-03 | 9.17e-03 | 49 |
GO:004885719 | Skin | cSCC | neural nucleus development | 28/4864 | 64/18723 | 1.52e-03 | 9.52e-03 | 28 |
GO:00324654 | Skin | cSCC | regulation of cytokinesis | 37/4864 | 92/18723 | 1.94e-03 | 1.17e-02 | 37 |
GO:001631115 | Skin | cSCC | dephosphorylation | 134/4864 | 417/18723 | 2.65e-03 | 1.50e-02 | 134 |
GO:003367425 | Skin | cSCC | positive regulation of kinase activity | 148/4864 | 467/18723 | 3.00e-03 | 1.66e-02 | 148 |
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 |
CALM3 | SNV | Missense_Mutation | novel | c.214N>T | p.Met72Leu | p.M72L | P62158 | protein_coding | tolerated_low_confidence(0.66) | benign(0.015) | TCGA-C5-A8YQ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Chemotherapy | cisplatin | PD |
CALM3 | SNV | Missense_Mutation | | c.27N>C | p.Gln9His | p.Q9H | P62158 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.625) | TCGA-DR-A0ZM-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unspecific | Cisplatin | SD |
CALM3 | SNV | Missense_Mutation | novel | c.150N>T | p.Gln50His | p.Q50H | P62158 | protein_coding | deleterious_low_confidence(0.05) | benign(0.054) | TCGA-MA-AA42-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
CALM3 | SNV | Missense_Mutation | novel | c.150G>T | p.Gln50His | p.Q50H | P62158 | protein_coding | deleterious_low_confidence(0.05) | benign(0.054) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CALM3 | SNV | Missense_Mutation | novel | c.31G>A | p.Ala11Thr | p.A11T | P62158 | protein_coding | deleterious_low_confidence(0.02) | benign(0.009) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
CALM3 | SNV | Missense_Mutation | novel | c.265G>A | p.Ala89Thr | p.A89T | P62158 | protein_coding | deleterious_low_confidence(0.01) | possibly_damaging(0.774) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
CALM3 | SNV | Missense_Mutation | novel | c.107T>C | p.Val36Ala | p.V36A | P62158 | protein_coding | deleterious_low_confidence(0.03) | possibly_damaging(0.842) | TCGA-B5-A3FA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CALM3 | SNV | Missense_Mutation | novel | c.319C>T | p.Arg107Cys | p.R107C | P62158 | protein_coding | tolerated_low_confidence(0.07) | benign(0.015) | TCGA-EY-A215-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CALM3 | SNV | Missense_Mutation | novel | c.35A>G | p.Glu12Gly | p.E12G | P62158 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.981) | TCGA-FI-A2F4-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CALM3 | SNV | Missense_Mutation | novel | c.178G>C | p.Gly60Arg | p.G60R | P62158 | protein_coding | deleterious_low_confidence(0.05) | possibly_damaging(0.654) | TCGA-37-A5EL-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | temodal | PD |