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Gene: YBX3 |
Gene summary for YBX3 |
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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 |
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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 |
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∗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 |
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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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GO ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | Count |
GO:0043487111 | Thyroid | PTC | regulation of RNA stability | 97/5968 | 170/18723 | 9.51e-12 | 3.97e-10 | 97 |
GO:0061013111 | Thyroid | PTC | regulation of mRNA catabolic process | 94/5968 | 166/18723 | 3.55e-11 | 1.29e-09 | 94 |
GO:0043488111 | Thyroid | PTC | regulation of mRNA stability | 90/5968 | 158/18723 | 5.98e-11 | 2.11e-09 | 90 |
GO:0001701111 | Thyroid | PTC | in utero embryonic development | 175/5968 | 367/18723 | 1.40e-10 | 4.73e-09 | 175 |
GO:0031330113 | Thyroid | PTC | negative regulation of cellular catabolic process | 131/5968 | 262/18723 | 6.63e-10 | 2.03e-08 | 131 |
GO:0009895113 | Thyroid | PTC | negative regulation of catabolic process | 154/5968 | 320/18723 | 7.77e-10 | 2.31e-08 | 154 |
GO:0071214111 | Thyroid | PTC | cellular response to abiotic stimulus | 158/5968 | 331/18723 | 9.90e-10 | 2.89e-08 | 158 |
GO:0104004111 | Thyroid | PTC | cellular response to environmental stimulus | 158/5968 | 331/18723 | 9.90e-10 | 2.89e-08 | 158 |
GO:2001243113 | Thyroid | PTC | negative regulation of intrinsic apoptotic signaling pathway | 60/5968 | 98/18723 | 2.05e-09 | 5.77e-08 | 60 |
GO:1903312113 | Thyroid | PTC | negative regulation of mRNA metabolic process | 53/5968 | 92/18723 | 3.03e-07 | 5.13e-06 | 53 |
GO:0061458112 | Thyroid | PTC | reproductive system development | 173/5968 | 427/18723 | 8.70e-05 | 7.23e-04 | 173 |
GO:0034612111 | Thyroid | PTC | response to tumor necrosis factor | 109/5968 | 253/18723 | 1.08e-04 | 8.69e-04 | 109 |
GO:0048608111 | Thyroid | PTC | reproductive structure development | 170/5968 | 424/18723 | 1.86e-04 | 1.41e-03 | 170 |
GO:00069709 | Thyroid | PTC | response to osmotic stress | 42/5968 | 84/18723 | 4.07e-04 | 2.73e-03 | 42 |
GO:1902369110 | Thyroid | PTC | negative regulation of RNA catabolic process | 38/5968 | 75/18723 | 5.41e-04 | 3.47e-03 | 38 |
GO:0071356111 | Thyroid | PTC | cellular response to tumor necrosis factor | 96/5968 | 229/18723 | 8.24e-04 | 5.10e-03 | 96 |
GO:00714743 | Thyroid | PTC | cellular hyperosmotic response | 11/5968 | 15/18723 | 1.19e-03 | 6.84e-03 | 11 |
GO:006053719 | Thyroid | PTC | muscle tissue development | 156/5968 | 403/18723 | 1.98e-03 | 1.06e-02 | 156 |
GO:00714709 | Thyroid | PTC | cellular response to osmotic stress | 22/5968 | 41/18723 | 3.11e-03 | 1.53e-02 | 22 |
GO:0006972 | Thyroid | PTC | hyperosmotic response | 16/5968 | 28/18723 | 4.99e-03 | 2.31e-02 | 16 |
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 |
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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 |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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