|
|||||
|
 | |
| |
| |
| |
| |
| |
|
Gene: YBX3 |
Gene summary for YBX3 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | YBX3 | Gene ID | 8531 |
| Gene name | Y-box binding protein 3 | |
| Gene Alias | CSDA | |
| Cytomap | 12p13.2 | |
| Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | A0A024RAV4 |
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 |
| 8531 | YBX3 | GSM4909282 | Human | Breast | IDC | 6.87e-23 | 5.39e-01 | -0.0288 |
| 8531 | YBX3 | GSM4909285 | Human | Breast | IDC | 6.01e-12 | -3.64e-01 | 0.21 |
| 8531 | YBX3 | GSM4909290 | Human | Breast | IDC | 7.06e-03 | -3.15e-01 | 0.2096 |
| 8531 | YBX3 | GSM4909291 | Human | Breast | IDC | 1.18e-14 | -6.16e-01 | 0.1753 |
| 8531 | YBX3 | GSM4909293 | Human | Breast | IDC | 8.79e-08 | -3.60e-01 | 0.1581 |
| 8531 | YBX3 | GSM4909294 | Human | Breast | IDC | 1.10e-20 | -5.66e-01 | 0.2022 |
| 8531 | YBX3 | GSM4909296 | Human | Breast | IDC | 1.06e-46 | -7.75e-01 | 0.1524 |
| 8531 | YBX3 | GSM4909297 | Human | Breast | IDC | 1.59e-32 | -6.36e-01 | 0.1517 |
| 8531 | YBX3 | GSM4909298 | Human | Breast | IDC | 1.82e-11 | -4.38e-01 | 0.1551 |
| 8531 | YBX3 | GSM4909301 | Human | Breast | IDC | 8.29e-48 | -8.07e-01 | 0.1577 |
| 8531 | YBX3 | GSM4909302 | Human | Breast | IDC | 1.01e-12 | -4.73e-01 | 0.1545 |
| 8531 | YBX3 | GSM4909304 | Human | Breast | IDC | 2.58e-05 | -3.32e-01 | 0.1636 |
| 8531 | YBX3 | GSM4909306 | Human | Breast | IDC | 2.68e-16 | -4.57e-01 | 0.1564 |
| 8531 | YBX3 | GSM4909307 | Human | Breast | IDC | 1.13e-29 | -6.49e-01 | 0.1569 |
| 8531 | YBX3 | GSM4909308 | Human | Breast | IDC | 2.60e-42 | -8.04e-01 | 0.158 |
| 8531 | YBX3 | GSM4909309 | Human | Breast | IDC | 4.73e-08 | -3.84e-01 | 0.0483 |
| 8531 | YBX3 | GSM4909311 | Human | Breast | IDC | 7.97e-52 | -6.90e-01 | 0.1534 |
| 8531 | YBX3 | GSM4909312 | Human | Breast | IDC | 2.66e-40 | -7.21e-01 | 0.1552 |
| 8531 | YBX3 | GSM4909313 | Human | Breast | IDC | 1.49e-06 | -3.72e-01 | 0.0391 |
| 8531 | YBX3 | GSM4909315 | Human | Breast | IDC | 1.32e-05 | -3.41e-01 | 0.21 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
| 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:006145823 | Cervix | N_HPV | reproductive system development | 23/534 | 427/18723 | 2.81e-03 | 2.45e-02 | 23 |
| GO:003133015 | Cervix | N_HPV | negative regulation of cellular catabolic process | 16/534 | 262/18723 | 3.63e-03 | 2.91e-02 | 16 |
| GO:006053722 | Cervix | N_HPV | muscle tissue development | 21/534 | 403/18723 | 6.10e-03 | 4.21e-02 | 21 |
| GO:004592713 | Cervix | N_HPV | positive regulation of growth | 15/534 | 259/18723 | 7.67e-03 | 4.96e-02 | 15 |
| GO:00466613 | Cervix | N_HPV | male sex differentiation | 11/534 | 165/18723 | 7.83e-03 | 4.97e-02 | 11 |
| GO:0002181 | Colorectum | AD | cytoplasmic translation | 109/3918 | 148/18723 | 3.40e-43 | 2.13e-39 | 109 |
| GO:1903311 | Colorectum | AD | regulation of mRNA metabolic process | 117/3918 | 288/18723 | 1.69e-14 | 4.23e-12 | 117 |
| GO:0009895 | Colorectum | AD | negative regulation of catabolic process | 124/3918 | 320/18723 | 1.66e-13 | 3.35e-11 | 124 |
| GO:0031330 | Colorectum | AD | negative regulation of cellular catabolic process | 104/3918 | 262/18723 | 2.66e-12 | 3.96e-10 | 104 |
| GO:0097193 | Colorectum | AD | intrinsic apoptotic signaling pathway | 108/3918 | 288/18723 | 6.25e-11 | 6.41e-09 | 108 |
| GO:0006401 | Colorectum | AD | RNA catabolic process | 102/3918 | 278/18723 | 8.64e-10 | 6.76e-08 | 102 |
| GO:0044270 | Colorectum | AD | cellular nitrogen compound catabolic process | 147/3918 | 451/18723 | 3.35e-09 | 2.23e-07 | 147 |
| GO:0046700 | Colorectum | AD | heterocycle catabolic process | 145/3918 | 445/18723 | 4.37e-09 | 2.84e-07 | 145 |
| GO:0006402 | Colorectum | AD | mRNA catabolic process | 87/3918 | 232/18723 | 4.40e-09 | 2.84e-07 | 87 |
| GO:2001242 | Colorectum | AD | regulation of intrinsic apoptotic signaling pathway | 67/3918 | 164/18723 | 4.94e-09 | 3.16e-07 | 67 |
| GO:0034655 | Colorectum | AD | nucleobase-containing compound catabolic process | 133/3918 | 407/18723 | 1.56e-08 | 9.12e-07 | 133 |
| GO:2001233 | Colorectum | AD | regulation of apoptotic signaling pathway | 119/3918 | 356/18723 | 2.14e-08 | 1.21e-06 | 119 |
| GO:0019439 | Colorectum | AD | aromatic compound catabolic process | 146/3918 | 467/18723 | 7.48e-08 | 3.84e-06 | 146 |
| GO:1901361 | Colorectum | AD | organic cyclic compound catabolic process | 153/3918 | 495/18723 | 8.23e-08 | 4.18e-06 | 153 |
| GO:0061013 | Colorectum | AD | regulation of mRNA catabolic process | 64/3918 | 166/18723 | 1.44e-07 | 6.59e-06 | 64 |
| 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 53 54 55 56 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0453018 | Breast | Precancer | Tight junction | 31/684 | 169/8465 | 1.13e-05 | 1.26e-04 | 9.64e-05 | 31 |
| hsa0453019 | Breast | Precancer | Tight junction | 31/684 | 169/8465 | 1.13e-05 | 1.26e-04 | 9.64e-05 | 31 |
| hsa0453024 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
| hsa0453034 | Breast | IDC | Tight junction | 38/867 | 169/8465 | 2.07e-06 | 3.20e-05 | 2.39e-05 | 38 |
| hsa0453044 | Breast | DCIS | Tight junction | 37/846 | 169/8465 | 3.07e-06 | 4.20e-05 | 3.09e-05 | 37 |
| hsa0453054 | Breast | DCIS | Tight junction | 37/846 | 169/8465 | 3.07e-06 | 4.20e-05 | 3.09e-05 | 37 |
| hsa0453020 | Cervix | CC | Tight junction | 49/1267 | 169/8465 | 1.87e-06 | 1.78e-05 | 1.05e-05 | 49 |
| hsa04530110 | Cervix | CC | Tight junction | 49/1267 | 169/8465 | 1.87e-06 | 1.78e-05 | 1.05e-05 | 49 |
| hsa04530 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
| hsa045301 | Colorectum | AD | Tight junction | 76/2092 | 169/8465 | 5.49e-09 | 9.69e-08 | 6.18e-08 | 76 |
| hsa045304 | Colorectum | MSS | Tight junction | 66/1875 | 169/8465 | 4.10e-07 | 6.25e-06 | 3.83e-06 | 66 |
| hsa045305 | Colorectum | MSS | Tight junction | 66/1875 | 169/8465 | 4.10e-07 | 6.25e-06 | 3.83e-06 | 66 |
| hsa045308 | Colorectum | FAP | Tight junction | 60/1404 | 169/8465 | 1.40e-09 | 9.33e-08 | 5.67e-08 | 60 |
| hsa045309 | Colorectum | FAP | Tight junction | 60/1404 | 169/8465 | 1.40e-09 | 9.33e-08 | 5.67e-08 | 60 |
| hsa0453026 | Endometrium | AEH | Tight junction | 54/1197 | 169/8465 | 1.99e-09 | 3.80e-08 | 2.78e-08 | 54 |
| hsa04530112 | Endometrium | AEH | Tight junction | 54/1197 | 169/8465 | 1.99e-09 | 3.80e-08 | 2.78e-08 | 54 |
| hsa0453027 | Endometrium | EEC | Tight junction | 54/1237 | 169/8465 | 6.56e-09 | 1.27e-07 | 9.46e-08 | 54 |
| hsa0453036 | Endometrium | EEC | Tight junction | 54/1237 | 169/8465 | 6.56e-09 | 1.27e-07 | 9.46e-08 | 54 |
| hsa04530211 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
| hsa04530310 | Esophagus | ESCC | Tight junction | 105/4205 | 169/8465 | 6.73e-04 | 2.23e-03 | 1.14e-03 | 105 |
| Page: 1 2 |
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 |
| YBX3 | SNV | Missense_Mutation | novel | c.928N>C | p.Asp310His | p.D310H | P16989 | protein_coding | deleterious(0) | probably_damaging(0.942) | TCGA-A2-A3Y0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
| YBX3 | SNV | Missense_Mutation | c.686G>A | p.Arg229His | p.R229H | P16989 | protein_coding | tolerated(0.07) | benign(0.402) | TCGA-EA-A3HU-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| YBX3 | SNV | Missense_Mutation | rs140201332 | c.980N>T | p.Arg327Leu | p.R327L | P16989 | protein_coding | deleterious(0.01) | benign(0.387) | TCGA-IR-A3LL-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
| YBX3 | SNV | Missense_Mutation | rs745797213 | c.863G>A | p.Arg288His | p.R288H | P16989 | protein_coding | deleterious(0.02) | benign(0.01) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
| YBX3 | SNV | Missense_Mutation | rs749620675 | c.584N>G | p.Glu195Gly | p.E195G | P16989 | protein_coding | tolerated(0.13) | probably_damaging(0.979) | TCGA-AA-A022-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| YBX3 | SNV | Missense_Mutation | c.947C>G | p.Ala316Gly | p.A316G | P16989 | protein_coding | tolerated(0.12) | benign(0.015) | TCGA-EI-6883-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Chemotherapy | 5fluorouracil+leucovorin | SD | |
| YBX3 | SNV | Missense_Mutation | novel | c.814N>T | p.Pro272Ser | p.P272S | P16989 | protein_coding | tolerated(0.21) | benign(0.074) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| YBX3 | SNV | Missense_Mutation | novel | c.265A>G | p.Thr89Ala | p.T89A | P16989 | protein_coding | tolerated(0.05) | benign(0.003) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| YBX3 | SNV | Missense_Mutation | novel | c.814C>T | p.Pro272Ser | p.P272S | P16989 | protein_coding | tolerated(0.21) | benign(0.074) | TCGA-A5-A0GG-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| YBX3 | SNV | Missense_Mutation | rs201062345 | c.893G>A | p.Arg298His | p.R298H | P16989 | protein_coding | tolerated(0.07) | benign(0.014) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 |
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 |