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/BMP4_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/BMP4_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/BMP4_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/BMP4_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/BMP4_pca_on_diff_genes.png) | EOLP: Erosive Oral lichen planus |
LP: leukoplakia |
NEOLP: Non-erosive oral lichen planus |
OSCC: Oral squamous cell carcinoma |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:00510984 | Colorectum | FAP | regulation of binding | 81/2622 | 363/18723 | 1.04e-05 | 2.97e-04 | 81 |
GO:00341014 | Colorectum | FAP | erythrocyte homeostasis | 37/2622 | 129/18723 | 1.06e-05 | 3.01e-04 | 37 |
GO:00486382 | Colorectum | FAP | regulation of developmental growth | 75/2622 | 330/18723 | 1.11e-05 | 3.10e-04 | 75 |
GO:00468224 | Colorectum | FAP | regulation of nucleocytoplasmic transport | 32/2622 | 106/18723 | 1.30e-05 | 3.53e-04 | 32 |
GO:00016673 | Colorectum | FAP | ameboidal-type cell migration | 100/2622 | 475/18723 | 1.42e-05 | 3.79e-04 | 100 |
GO:00513484 | Colorectum | FAP | negative regulation of transferase activity | 63/2622 | 268/18723 | 1.82e-05 | 4.57e-04 | 63 |
GO:19028933 | Colorectum | FAP | regulation of pri-miRNA transcription by RNA polymerase II | 20/2622 | 54/18723 | 2.09e-05 | 5.05e-04 | 20 |
GO:00226123 | Colorectum | FAP | gland morphogenesis | 34/2622 | 118/18723 | 2.13e-05 | 5.12e-04 | 34 |
GO:00323864 | Colorectum | FAP | regulation of intracellular transport | 75/2622 | 337/18723 | 2.38e-05 | 5.60e-04 | 75 |
GO:00302184 | Colorectum | FAP | erythrocyte differentiation | 34/2622 | 120/18723 | 3.13e-05 | 7.11e-04 | 34 |
GO:00331574 | Colorectum | FAP | regulation of intracellular protein transport | 55/2622 | 229/18723 | 3.20e-05 | 7.20e-04 | 55 |
GO:00345044 | Colorectum | FAP | protein localization to nucleus | 66/2622 | 290/18723 | 3.47e-05 | 7.64e-04 | 66 |
GO:00719003 | Colorectum | FAP | regulation of protein serine/threonine kinase activity | 78/2622 | 359/18723 | 3.99e-05 | 8.48e-04 | 78 |
GO:00019334 | Colorectum | FAP | negative regulation of protein phosphorylation | 75/2622 | 342/18723 | 4.02e-05 | 8.53e-04 | 75 |
GO:00351962 | Colorectum | FAP | production of miRNAs involved in gene silencing by miRNA | 19/2622 | 52/18723 | 4.16e-05 | 8.78e-04 | 19 |
GO:00459364 | Colorectum | FAP | negative regulation of phosphate metabolic process | 92/2622 | 441/18723 | 4.43e-05 | 9.26e-04 | 92 |
GO:00510994 | Colorectum | FAP | positive regulation of binding | 44/2622 | 173/18723 | 4.52e-05 | 9.40e-04 | 44 |
GO:00105634 | Colorectum | FAP | negative regulation of phosphorus metabolic process | 92/2622 | 442/18723 | 4.84e-05 | 9.91e-04 | 92 |
GO:00703022 | Colorectum | FAP | regulation of stress-activated protein kinase signaling cascade | 48/2622 | 195/18723 | 5.14e-05 | 1.04e-03 | 48 |
GO:00064693 | Colorectum | FAP | negative regulation of protein kinase activity | 51/2622 | 212/18723 | 5.82e-05 | 1.15e-03 | 51 |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa04919 | Colorectum | AD | Thyroid hormone signaling pathway | 51/2092 | 121/8465 | 1.71e-05 | 1.73e-04 | 1.10e-04 | 51 |
hsa05418 | Colorectum | AD | Fluid shear stress and atherosclerosis | 54/2092 | 139/8465 | 1.41e-04 | 1.16e-03 | 7.37e-04 | 54 |
hsa049191 | Colorectum | AD | Thyroid hormone signaling pathway | 51/2092 | 121/8465 | 1.71e-05 | 1.73e-04 | 1.10e-04 | 51 |
hsa054181 | Colorectum | AD | Fluid shear stress and atherosclerosis | 54/2092 | 139/8465 | 1.41e-04 | 1.16e-03 | 7.37e-04 | 54 |
hsa049192 | Colorectum | SER | Thyroid hormone signaling pathway | 40/1580 | 121/8465 | 1.02e-04 | 1.06e-03 | 7.67e-04 | 40 |
hsa054182 | Colorectum | SER | Fluid shear stress and atherosclerosis | 40/1580 | 139/8465 | 2.28e-03 | 1.75e-02 | 1.27e-02 | 40 |
hsa049193 | Colorectum | SER | Thyroid hormone signaling pathway | 40/1580 | 121/8465 | 1.02e-04 | 1.06e-03 | 7.67e-04 | 40 |
hsa054183 | Colorectum | SER | Fluid shear stress and atherosclerosis | 40/1580 | 139/8465 | 2.28e-03 | 1.75e-02 | 1.27e-02 | 40 |
hsa049194 | Colorectum | MSS | Thyroid hormone signaling pathway | 46/1875 | 121/8465 | 5.04e-05 | 4.97e-04 | 3.05e-04 | 46 |
hsa054184 | Colorectum | MSS | Fluid shear stress and atherosclerosis | 51/1875 | 139/8465 | 6.06e-05 | 5.80e-04 | 3.55e-04 | 51 |
hsa04390 | Colorectum | MSS | Hippo signaling pathway | 48/1875 | 157/8465 | 8.32e-03 | 3.10e-02 | 1.90e-02 | 48 |
hsa049195 | Colorectum | MSS | Thyroid hormone signaling pathway | 46/1875 | 121/8465 | 5.04e-05 | 4.97e-04 | 3.05e-04 | 46 |
hsa054185 | Colorectum | MSS | Fluid shear stress and atherosclerosis | 51/1875 | 139/8465 | 6.06e-05 | 5.80e-04 | 3.55e-04 | 51 |
hsa043901 | Colorectum | MSS | Hippo signaling pathway | 48/1875 | 157/8465 | 8.32e-03 | 3.10e-02 | 1.90e-02 | 48 |
hsa054186 | Colorectum | MSI-H | Fluid shear stress and atherosclerosis | 25/797 | 139/8465 | 1.11e-03 | 1.20e-02 | 1.01e-02 | 25 |
hsa049196 | Colorectum | MSI-H | Thyroid hormone signaling pathway | 21/797 | 121/8465 | 4.18e-03 | 4.10e-02 | 3.44e-02 | 21 |
hsa054187 | Colorectum | MSI-H | Fluid shear stress and atherosclerosis | 25/797 | 139/8465 | 1.11e-03 | 1.20e-02 | 1.01e-02 | 25 |
hsa049197 | Colorectum | MSI-H | Thyroid hormone signaling pathway | 21/797 | 121/8465 | 4.18e-03 | 4.10e-02 | 3.44e-02 | 21 |
hsa049198 | Colorectum | FAP | Thyroid hormone signaling pathway | 41/1404 | 121/8465 | 2.28e-06 | 4.28e-05 | 2.60e-05 | 41 |
hsa054188 | Colorectum | FAP | Fluid shear stress and atherosclerosis | 45/1404 | 139/8465 | 3.05e-06 | 4.63e-05 | 2.81e-05 | 45 |
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 |
BMP4 | SNV | Missense_Mutation | | c.404A>T | p.Asn135Ile | p.N135I | P12644 | protein_coding | tolerated(0.12) | benign(0.1) | TCGA-AN-A0AR-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
BMP4 | SNV | Missense_Mutation | rs747238009 | c.340N>T | p.Ala114Ser | p.A114S | P12644 | protein_coding | deleterious(0.04) | probably_damaging(0.999) | TCGA-E9-A295-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
BMP4 | deletion | Frame_Shift_Del | novel | c.179delN | p.Thr60AsnfsTer58 | p.T60Nfs*58 | P12644 | protein_coding | | | TCGA-D8-A27V-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD |
BMP4 | SNV | Missense_Mutation | rs750868626 | c.1223N>A | p.Arg408His | p.R408H | P12644 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
BMP4 | SNV | Missense_Mutation | rs773416502 | c.484N>T | p.Arg162Trp | p.R162W | P12644 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
BMP4 | SNV | Missense_Mutation | novel | c.646N>C | p.Asp216His | p.D216H | P12644 | protein_coding | deleterious(0) | probably_damaging(0.946) | TCGA-C5-A2LZ-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Unknown | Unknown | PD |
BMP4 | SNV | Missense_Mutation | | c.464N>G | p.Ser155Cys | p.S155C | P12644 | protein_coding | deleterious(0.01) | probably_damaging(0.976) | TCGA-IR-A3LL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
BMP4 | SNV | Missense_Mutation | | c.313N>C | p.Glu105Gln | p.E105Q | P12644 | protein_coding | tolerated(0.7) | benign(0.015) | TCGA-UC-A7PF-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
BMP4 | SNV | Missense_Mutation | novel | c.239N>T | p.Pro80Leu | p.P80L | P12644 | protein_coding | deleterious(0) | probably_damaging(0.995) | TCGA-VS-A959-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD |
BMP4 | SNV | Missense_Mutation | novel | c.1154A>G | p.Tyr385Cys | p.Y385C | P12644 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |