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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 |
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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 |
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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. |
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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). |
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Enriched GO biological processes. |
GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:000697016 | Thyroid | ATC | response to osmotic stress | 45/6293 | 84/18723 | 1.27e-04 | 9.03e-04 | 45 |
GO:004666112 | Thyroid | ATC | male sex differentiation | 77/6293 | 165/18723 | 3.27e-04 | 2.04e-03 | 77 |
GO:007135627 | Thyroid | ATC | cellular response to tumor necrosis factor | 102/6293 | 229/18723 | 3.52e-04 | 2.18e-03 | 102 |
GO:000751716 | Thyroid | ATC | muscle organ development | 139/6293 | 327/18723 | 4.45e-04 | 2.64e-03 | 139 |
GO:190236923 | Thyroid | ATC | negative regulation of RNA catabolic process | 39/6293 | 75/18723 | 7.65e-04 | 4.23e-03 | 39 |
GO:000840613 | Thyroid | ATC | gonad development | 96/6293 | 221/18723 | 1.40e-03 | 7.25e-03 | 96 |
GO:007147412 | Thyroid | ATC | cellular hyperosmotic response | 11/6293 | 15/18723 | 1.94e-03 | 9.41e-03 | 11 |
GO:004863815 | Thyroid | ATC | regulation of developmental growth | 136/6293 | 330/18723 | 2.17e-03 | 1.02e-02 | 136 |
GO:00451374 | Thyroid | ATC | development of primary sexual characteristics | 97/6293 | 227/18723 | 2.47e-03 | 1.14e-02 | 97 |
GO:007147015 | Thyroid | ATC | cellular response to osmotic stress | 23/6293 | 41/18723 | 2.53e-03 | 1.16e-02 | 23 |
GO:00352654 | Thyroid | ATC | organ growth | 77/6293 | 178/18723 | 4.45e-03 | 1.85e-02 | 77 |
GO:004592720 | Thyroid | ATC | positive regulation of growth | 106/6293 | 259/18723 | 7.90e-03 | 3.06e-02 | 106 |
GO:006053814 | Thyroid | ATC | skeletal muscle organ development | 71/6293 | 166/18723 | 8.39e-03 | 3.22e-02 | 71 |
GO:00069721 | Thyroid | ATC | hyperosmotic response | 16/6293 | 28/18723 | 8.86e-03 | 3.36e-02 | 16 |
GO:007026512 | Thyroid | ATC | necrotic cell death | 30/6293 | 62/18723 | 1.12e-02 | 4.00e-02 | 30 |
GO:000751913 | Thyroid | ATC | skeletal muscle tissue development | 66/6293 | 155/18723 | 1.20e-02 | 4.27e-02 | 66 |
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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 |
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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 |
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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. |
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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 |
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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 |
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