|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: UBB |
Gene summary for UBB |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | UBB | Gene ID | 7314 |
| Gene name | ubiquitin B | |
| Gene Alias | HEL-S-50 | |
| Cytomap | 17p11.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P0CG47 |
Top |
Malignant transformation analysis |
| Identification of the aberrant gene expression in precancerous and cancerous lesions by comparing the gene expression of stem-like cells in diseased tissues with normal stem cells |
| Malignant transformation involving gene list. |
| Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
| 7314 | UBB | GSM4909277 | Human | Breast | Precancer | 1.09e-09 | 7.00e-01 | 0.0177 |
| 7314 | UBB | GSM4909280 | Human | Breast | Precancer | 1.03e-09 | 5.37e-01 | 0.0305 |
| 7314 | UBB | GSM4909286 | Human | Breast | IDC | 8.44e-08 | -1.29e-01 | 0.1081 |
| 7314 | UBB | GSM4909291 | Human | Breast | IDC | 1.56e-14 | 4.41e-01 | 0.1753 |
| 7314 | UBB | GSM4909293 | Human | Breast | IDC | 5.37e-09 | -1.82e-01 | 0.1581 |
| 7314 | UBB | GSM4909294 | Human | Breast | IDC | 9.65e-05 | 8.74e-02 | 0.2022 |
| 7314 | UBB | GSM4909295 | Human | Breast | IDC | 4.96e-04 | 3.37e-01 | 0.0898 |
| 7314 | UBB | GSM4909297 | Human | Breast | IDC | 1.21e-20 | 2.35e-01 | 0.1517 |
| 7314 | UBB | GSM4909298 | Human | Breast | IDC | 2.05e-14 | -3.92e-01 | 0.1551 |
| 7314 | UBB | GSM4909302 | Human | Breast | IDC | 2.15e-03 | -3.61e-01 | 0.1545 |
| 7314 | UBB | GSM4909305 | Human | Breast | IDC | 2.80e-02 | 1.82e-01 | 0.0436 |
| 7314 | UBB | GSM4909308 | Human | Breast | IDC | 7.35e-03 | 2.01e-01 | 0.158 |
| 7314 | UBB | GSM4909311 | Human | Breast | IDC | 7.54e-40 | -6.90e-01 | 0.1534 |
| 7314 | UBB | GSM4909312 | Human | Breast | IDC | 2.00e-11 | -4.56e-01 | 0.1552 |
| 7314 | UBB | GSM4909315 | Human | Breast | IDC | 7.81e-05 | -3.29e-01 | 0.21 |
| 7314 | UBB | GSM4909317 | Human | Breast | IDC | 3.60e-07 | 3.15e-01 | 0.1355 |
| 7314 | UBB | GSM4909319 | Human | Breast | IDC | 1.70e-47 | -5.26e-01 | 0.1563 |
| 7314 | UBB | GSM4909321 | Human | Breast | IDC | 9.23e-44 | 5.66e-01 | 0.1559 |
| 7314 | UBB | brca3 | Human | Breast | Precancer | 8.90e-08 | -1.48e-01 | -0.0263 |
| 7314 | UBB | NCCBC14 | Human | Breast | DCIS | 4.62e-06 | -3.06e-01 | 0.2021 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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. |
Top |
Malignant transformation related pathway analysis |
| Find out the enriched GO biological processes and KEGG pathways involved in transition from healthy to precancer to cancer |
| Figure of enriched GO biological processes. |
| Tissue | Disease Stage | Enriched GO biological Processes |
| Colorectum | AD |  |
| Colorectum | SER |  |
| Colorectum | MSS |  |
| Colorectum | MSI-H |  |
| Colorectum | FAP |  |
| ∗Top 15 enriched GO BP terms are showed in the bar plot of each disease state in each tissue. Each row represents a significant GO biological process which is colored according to the -log10(p.adjust). |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched GO biological processes. |
| GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
| GO:00971939 | Breast | Precancer | intrinsic apoptotic signaling pathway | 59/1080 | 288/18723 | 8.07e-18 | 3.60e-15 | 59 |
| GO:20012339 | Breast | Precancer | regulation of apoptotic signaling pathway | 65/1080 | 356/18723 | 7.70e-17 | 3.17e-14 | 65 |
| GO:20012429 | Breast | Precancer | regulation of intrinsic apoptotic signaling pathway | 41/1080 | 164/18723 | 6.48e-16 | 2.31e-13 | 41 |
| GO:00709979 | Breast | Precancer | neuron death | 50/1080 | 361/18723 | 7.75e-09 | 5.70e-07 | 50 |
| GO:20012445 | Breast | Precancer | positive regulation of intrinsic apoptotic signaling pathway | 17/1080 | 58/18723 | 1.59e-08 | 1.12e-06 | 17 |
| GO:19033209 | Breast | Precancer | regulation of protein modification by small protein conjugation or removal | 38/1080 | 242/18723 | 1.71e-08 | 1.17e-06 | 38 |
| GO:00313969 | Breast | Precancer | regulation of protein ubiquitination | 33/1080 | 210/18723 | 1.45e-07 | 7.82e-06 | 33 |
| GO:00518816 | Breast | Precancer | regulation of mitochondrial membrane potential | 18/1080 | 74/18723 | 1.45e-07 | 7.82e-06 | 18 |
| GO:00104989 | Breast | Precancer | proteasomal protein catabolic process | 58/1080 | 490/18723 | 1.54e-07 | 8.05e-06 | 58 |
| GO:20012356 | Breast | Precancer | positive regulation of apoptotic signaling pathway | 24/1080 | 126/18723 | 1.98e-07 | 1.01e-05 | 24 |
| GO:19017989 | Breast | Precancer | positive regulation of signal transduction by p53 class mediator | 10/1080 | 25/18723 | 5.77e-07 | 2.49e-05 | 10 |
| GO:19033629 | Breast | Precancer | regulation of cellular protein catabolic process | 36/1080 | 255/18723 | 6.03e-07 | 2.55e-05 | 36 |
| GO:19017969 | Breast | Precancer | regulation of signal transduction by p53 class mediator | 19/1080 | 93/18723 | 1.20e-06 | 4.60e-05 | 19 |
| GO:19012149 | Breast | Precancer | regulation of neuron death | 41/1080 | 319/18723 | 1.27e-06 | 4.80e-05 | 41 |
| GO:00421769 | Breast | Precancer | regulation of protein catabolic process | 47/1080 | 391/18723 | 1.50e-06 | 5.58e-05 | 47 |
| GO:00723319 | Breast | Precancer | signal transduction by p53 class mediator | 26/1080 | 163/18723 | 2.23e-06 | 7.76e-05 | 26 |
| GO:19030509 | Breast | Precancer | regulation of proteolysis involved in cellular protein catabolic process | 31/1080 | 221/18723 | 4.10e-06 | 1.27e-04 | 31 |
| GO:00723328 | Breast | Precancer | intrinsic apoptotic signaling pathway by p53 class mediator | 16/1080 | 76/18723 | 5.49e-06 | 1.63e-04 | 16 |
| GO:19022537 | Breast | Precancer | regulation of intrinsic apoptotic signaling pathway by p53 class mediator | 9/1080 | 29/18723 | 2.40e-05 | 5.53e-04 | 9 |
| GO:00611369 | Breast | Precancer | regulation of proteasomal protein catabolic process | 24/1080 | 187/18723 | 1.99e-04 | 3.14e-03 | 24 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 |
| Enriched KEGG pathways. |
| 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 |
| hsa0502216 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
| hsa0513118 | Breast | Precancer | Shigellosis | 44/684 | 247/8465 | 3.91e-07 | 6.86e-06 | 5.26e-06 | 44 |
| hsa0516718 | Breast | Precancer | Kaposi sarcoma-associated herpesvirus infection | 36/684 | 194/8465 | 1.68e-06 | 2.53e-05 | 1.94e-05 | 36 |
| hsa0413716 | Breast | Precancer | Mitophagy - animal | 15/684 | 72/8465 | 5.22e-04 | 3.93e-03 | 3.01e-03 | 15 |
| hsa0501219 | Breast | Precancer | Parkinson disease | 99/684 | 266/8465 | 3.58e-42 | 5.65e-40 | 4.33e-40 | 99 |
| hsa0502217 | Breast | Precancer | Pathways of neurodegeneration - multiple diseases | 112/684 | 476/8465 | 6.96e-27 | 2.44e-25 | 1.87e-25 | 112 |
| hsa0513119 | Breast | Precancer | Shigellosis | 44/684 | 247/8465 | 3.91e-07 | 6.86e-06 | 5.26e-06 | 44 |
| hsa0516719 | Breast | Precancer | Kaposi sarcoma-associated herpesvirus infection | 36/684 | 194/8465 | 1.68e-06 | 2.53e-05 | 1.94e-05 | 36 |
| hsa0413717 | Breast | Precancer | Mitophagy - animal | 15/684 | 72/8465 | 5.22e-04 | 3.93e-03 | 3.01e-03 | 15 |
| hsa0501224 | Breast | IDC | Parkinson disease | 107/867 | 266/8465 | 2.57e-39 | 8.36e-37 | 6.26e-37 | 107 |
| hsa0502223 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
| hsa0513124 | Breast | IDC | Shigellosis | 47/867 | 247/8465 | 1.78e-05 | 2.00e-04 | 1.49e-04 | 47 |
| hsa0516723 | Breast | IDC | Kaposi sarcoma-associated herpesvirus infection | 38/867 | 194/8465 | 5.87e-05 | 5.96e-04 | 4.46e-04 | 38 |
| hsa0413723 | Breast | IDC | Mitophagy - animal | 17/867 | 72/8465 | 7.61e-04 | 6.04e-03 | 4.52e-03 | 17 |
| hsa0501234 | Breast | IDC | Parkinson disease | 107/867 | 266/8465 | 2.57e-39 | 8.36e-37 | 6.26e-37 | 107 |
| hsa0502233 | Breast | IDC | Pathways of neurodegeneration - multiple diseases | 116/867 | 476/8465 | 3.63e-20 | 1.18e-18 | 8.82e-19 | 116 |
| hsa0513134 | Breast | IDC | Shigellosis | 47/867 | 247/8465 | 1.78e-05 | 2.00e-04 | 1.49e-04 | 47 |
| hsa0516733 | Breast | IDC | Kaposi sarcoma-associated herpesvirus infection | 38/867 | 194/8465 | 5.87e-05 | 5.96e-04 | 4.46e-04 | 38 |
| hsa0413733 | Breast | IDC | Mitophagy - animal | 17/867 | 72/8465 | 7.61e-04 | 6.04e-03 | 4.52e-03 | 17 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 |
Top |
Cell-cell communication analysis |
| Identification of potential cell-cell interactions between two cell types and their ligand-receptor pairs for different disease states |
| Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
| Page: 1 |
Top |
Single-cell gene regulatory network inference analysis |
| Find out the significant the regulons (TFs) and the target genes of each regulon across cell types for different disease states |
| TF | Cell Type | Tissue | Disease Stage | Target Gene | RSS | Regulon Activity |
| ∗The dot plots of a searched regulon are shown for all cell subpopulations in each disease state of each tissue based on the regulon specific score inferred using pySCENIC and by calculating the average expression. |
| Page: 1 |
Top |
Somatic mutation of malignant transformation related genes |
| Annotation of somatic variants for genes involved in malignant transformation |
| 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 |
| UBB | SNV | Missense_Mutation | c.70N>C | p.Glu24Gln | p.E24Q | P0CG47 | protein_coding | tolerated(0.2) | benign(0.047) | TCGA-HM-A4S6-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Chemotherapy | cisplatin | CR | |
| UBB | SNV | Missense_Mutation | c.65N>T | p.Thr22Ile | p.T22I | P0CG47 | protein_coding | deleterious(0.01) | possibly_damaging(0.49) | TCGA-QG-A5Z2-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| UBB | SNV | Missense_Mutation | c.388N>T | p.Arg130Cys | p.R130C | P0CG47 | protein_coding | tolerated(0.07) | benign(0.198) | TCGA-AG-A01Y-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| UBB | SNV | Missense_Mutation | c.671N>A | p.Arg224His | p.R224H | P0CG47 | protein_coding | deleterious(0.04) | possibly_damaging(0.867) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
| UBB | SNV | Missense_Mutation | c.328N>A | p.Glu110Lys | p.E110K | P0CG47 | protein_coding | deleterious(0.02) | benign(0.268) | TCGA-AP-A1E0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD | |
| UBB | SNV | Missense_Mutation | novel | c.355N>A | p.Leu119Ile | p.L119I | P0CG47 | protein_coding | deleterious(0.02) | possibly_damaging(0.645) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
| UBB | SNV | Missense_Mutation | c.93G>T | p.Gln31His | p.Q31H | P0CG47 | protein_coding | tolerated(0.05) | benign(0.031) | TCGA-AX-A2H5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Chemotherapy | carboplatin | CR | |
| UBB | SNV | Missense_Mutation | novel | c.179N>G | p.Asn60Ser | p.N60S | P0CG47 | protein_coding | tolerated(0.17) | benign(0.003) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| UBB | SNV | Missense_Mutation | novel | c.443N>A | p.Arg148His | p.R148H | P0CG47 | protein_coding | tolerated(0.08) | possibly_damaging(0.9) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| UBB | SNV | Missense_Mutation | novel | c.292N>G | p.Thr98Ala | p.T98A | P0CG47 | protein_coding | deleterious(0.01) | benign(0.13) | TCGA-BG-A221-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 |
Top |
Related drugs of malignant transformation related genes |
| Identification of chemicals and drugs interact with genes involved in malignant transfromation |
| (DGIdb 4.0) |
| Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
| Page: 1 |
Copyright 2023-Present -The University of Texas Health Science Center at Houston |