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/CALML3_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/CALML3_pca_on_diff_genes.png) | CC: Cervix cancer |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions |
N_HPV: HPV-infected normal cervix |
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/CALML3_pca_on_diff_genes.png) | ESCC: Esophageal squamous cell carcinoma |
HGIN: High-grade intraepithelial neoplasias |
LGIN: Low-grade intraepithelial neoplasias |
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/CALML3_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
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/CALML3_pca_on_diff_genes.png) | AK: Actinic keratosis |
cSCC: Cutaneous squamous cell carcinoma |
SCCIS:squamous cell carcinoma in situ |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0541834 | Breast | IDC | Fluid shear stress and atherosclerosis | 34/867 | 139/8465 | 9.41e-07 | 1.61e-05 | 1.20e-05 | 34 |
hsa0421834 | Breast | IDC | Cellular senescence | 35/867 | 156/8465 | 5.49e-06 | 7.43e-05 | 5.56e-05 | 35 |
hsa0516733 | Breast | IDC | Kaposi sarcoma-associated herpesvirus infection | 38/867 | 194/8465 | 5.87e-05 | 5.96e-04 | 4.46e-04 | 38 |
hsa050313 | Breast | IDC | Amphetamine addiction | 18/867 | 69/8465 | 1.42e-04 | 1.36e-03 | 1.01e-03 | 18 |
hsa0516334 | Breast | IDC | Human cytomegalovirus infection | 39/867 | 225/8465 | 6.66e-04 | 5.41e-03 | 4.05e-03 | 39 |
hsa0521413 | Breast | IDC | Glioma | 16/867 | 75/8465 | 3.30e-03 | 2.10e-02 | 1.57e-02 | 16 |
hsa0541734 | Breast | IDC | Lipid and atherosclerosis | 35/867 | 215/8465 | 3.67e-03 | 2.29e-02 | 1.71e-02 | 35 |
hsa0497132 | Breast | IDC | Gastric acid secretion | 16/867 | 76/8465 | 3.80e-03 | 2.33e-02 | 1.74e-02 | 16 |
hsa0497011 | Breast | IDC | Salivary secretion | 18/867 | 93/8465 | 5.69e-03 | 3.13e-02 | 2.34e-02 | 18 |
hsa0517015 | Breast | IDC | Human immunodeficiency virus 1 infection | 33/867 | 212/8465 | 9.28e-03 | 4.37e-02 | 3.27e-02 | 33 |
hsa0501243 | Breast | DCIS | Parkinson disease | 106/846 | 266/8465 | 1.64e-39 | 5.29e-37 | 3.90e-37 | 106 |
hsa0501043 | Breast | DCIS | Alzheimer disease | 105/846 | 384/8465 | 3.23e-23 | 1.49e-21 | 1.10e-21 | 105 |
hsa0502243 | Breast | DCIS | Pathways of neurodegeneration - multiple diseases | 114/846 | 476/8465 | 4.74e-20 | 1.53e-18 | 1.13e-18 | 114 |
hsa0491542 | Breast | DCIS | Estrogen signaling pathway | 35/846 | 138/8465 | 1.40e-07 | 2.51e-06 | 1.85e-06 | 35 |
hsa0541844 | Breast | DCIS | Fluid shear stress and atherosclerosis | 34/846 | 139/8465 | 5.31e-07 | 9.03e-06 | 6.65e-06 | 34 |
hsa0421844 | Breast | DCIS | Cellular senescence | 34/846 | 156/8465 | 8.53e-06 | 1.06e-04 | 7.80e-05 | 34 |
hsa0516743 | Breast | DCIS | Kaposi sarcoma-associated herpesvirus infection | 38/846 | 194/8465 | 3.43e-05 | 3.69e-04 | 2.72e-04 | 38 |
hsa050314 | Breast | DCIS | Amphetamine addiction | 17/846 | 69/8465 | 3.37e-04 | 2.72e-03 | 2.00e-03 | 17 |
hsa0516344 | Breast | DCIS | Human cytomegalovirus infection | 38/846 | 225/8465 | 8.11e-04 | 5.95e-03 | 4.38e-03 | 38 |
hsa0521422 | Breast | DCIS | Glioma | 16/846 | 75/8465 | 2.58e-03 | 1.63e-02 | 1.20e-02 | 16 |
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 |
CALML3 | SNV | Missense_Mutation | | c.91N>T | p.Arg31Cys | p.R31C | P27482 | protein_coding | deleterious_low_confidence(0) | benign(0.046) | TCGA-D8-A142-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | cyclophosphamid | SD |
CALML3 | insertion | Frame_Shift_Ins | novel | c.436_437insTTCA | p.Val147HisfsTer47 | p.V147Hfs*47 | P27482 | protein_coding | | | TCGA-DS-A1OB-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | carboplatin | PD |
CALML3 | SNV | Missense_Mutation | | c.58N>A | p.Phe20Ile | p.F20I | P27482 | protein_coding | deleterious_low_confidence(0.01) | benign(0.406) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CALML3 | SNV | Missense_Mutation | | c.219N>T | p.Met73Ile | p.M73I | P27482 | protein_coding | deleterious_low_confidence(0.03) | benign(0.122) | TCGA-G4-6309-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Chemotherapy | xeloda | PD |
CALML3 | SNV | Missense_Mutation | | c.134C>T | p.Thr45Met | p.T45M | P27482 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.717) | TCGA-EI-6882-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
CALML3 | SNV | Missense_Mutation | | c.220N>A | p.Ala74Thr | p.A74T | P27482 | protein_coding | deleterious_low_confidence(0.03) | benign(0.036) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CALML3 | SNV | Missense_Mutation | novel | c.152N>G | p.Asp51Gly | p.D51G | P27482 | protein_coding | tolerated_low_confidence(0.06) | benign(0.001) | TCGA-AP-A0LD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CALML3 | SNV | Missense_Mutation | novel | c.51C>A | p.Phe17Leu | p.F17L | P27482 | protein_coding | deleterious_low_confidence(0.03) | probably_damaging(0.953) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
CALML3 | SNV | Missense_Mutation | rs754327442 | c.379C>T | p.Arg127Trp | p.R127W | P27482 | protein_coding | deleterious_low_confidence(0.01) | probably_damaging(0.989) | TCGA-BG-A0MQ-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
CALML3 | SNV | Missense_Mutation | rs752809700 | c.386N>T | p.Ala129Val | p.A129V | P27482 | protein_coding | deleterious_low_confidence(0.02) | possibly_damaging(0.715) | TCGA-BG-A220-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |