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Gene: RPS4X |
Gene summary for RPS4X |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPS4X | Gene ID | 6191 |
| Gene name | ribosomal protein S4 X-linked | |
| Gene Alias | CCG2 | |
| Cytomap | Xq13.1 | |
| Gene Type | protein-coding | GO ID | GO:0002181 | UniProtAcc | B2R491 |
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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 |
| 6191 | RPS4X | GSM4909315 | Human | Breast | IDC | 2.82e-69 | -4.31e-01 | 0.21 |
| 6191 | RPS4X | GSM4909316 | Human | Breast | IDC | 8.02e-34 | -6.88e-01 | 0.21 |
| 6191 | RPS4X | GSM4909317 | Human | Breast | IDC | 4.73e-24 | -2.54e-01 | 0.1355 |
| 6191 | RPS4X | GSM4909318 | Human | Breast | IDC | 3.93e-05 | -2.72e-01 | 0.2031 |
| 6191 | RPS4X | GSM4909319 | Human | Breast | IDC | 1.10e-47 | -5.99e-01 | 0.1563 |
| 6191 | RPS4X | GSM4909320 | Human | Breast | IDC | 3.04e-13 | -3.18e-01 | 0.1575 |
| 6191 | RPS4X | GSM4909321 | Human | Breast | IDC | 4.28e-30 | -2.17e-01 | 0.1559 |
| 6191 | RPS4X | brca2 | Human | Breast | Precancer | 1.17e-32 | -1.83e-01 | -0.024 |
| 6191 | RPS4X | brca3 | Human | Breast | Precancer | 1.40e-17 | -9.59e-02 | -0.0263 |
| 6191 | RPS4X | brca10 | Human | Breast | Precancer | 9.80e-13 | -1.62e-01 | -0.0029 |
| 6191 | RPS4X | M1 | Human | Breast | IDC | 6.08e-06 | -1.28e-01 | 0.1577 |
| 6191 | RPS4X | M2 | Human | Breast | IDC | 1.94e-21 | -5.05e-01 | 0.21 |
| 6191 | RPS4X | M5 | Human | Breast | IDC | 1.65e-03 | -2.90e-01 | 0.1598 |
| 6191 | RPS4X | NCCBC14 | Human | Breast | DCIS | 2.83e-25 | -3.33e-01 | 0.2021 |
| 6191 | RPS4X | NCCBC2 | Human | Breast | DCIS | 3.07e-04 | -2.90e-01 | 0.1554 |
| 6191 | RPS4X | NCCBC3 | Human | Breast | DCIS | 1.54e-07 | -4.94e-02 | 0.1198 |
| 6191 | RPS4X | NCCBC5 | Human | Breast | DCIS | 3.51e-29 | -3.51e-01 | 0.2046 |
| 6191 | RPS4X | P1 | Human | Breast | IDC | 2.10e-57 | -7.38e-01 | 0.1527 |
| 6191 | RPS4X | P2 | Human | Breast | IDC | 4.94e-25 | -3.76e-01 | 0.21 |
| 6191 | RPS4X | CA_HPV_1 | Human | Cervix | CC | 2.00e-15 | -2.72e-01 | 0.0264 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 |
| 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 | ||
| GC |  | CAG: Chronic atrophic gastritis |
| CAG with IM: Chronic atrophic gastritis with intestinal metaplasia | ||
| CSG: Chronic superficial gastritis | ||
| GC: Gastric cancer | ||
| SIM: Severe intestinal metaplasia | ||
| WIM: Wild intestinal metaplasia | ||
| 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. |
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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). |
| 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:00021819 | Breast | Precancer | cytoplasmic translation | 80/1080 | 148/18723 | 1.59e-59 | 8.54e-56 | 80 |
| GO:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
| GO:00457279 | Breast | Precancer | positive regulation of translation | 32/1080 | 136/18723 | 5.89e-12 | 9.27e-10 | 32 |
| GO:00342509 | Breast | Precancer | positive regulation of cellular amide metabolic process | 33/1080 | 162/18723 | 1.72e-10 | 1.77e-08 | 33 |
| GO:000218114 | Breast | IDC | cytoplasmic translation | 82/1434 | 148/18723 | 2.60e-52 | 1.48e-48 | 82 |
| GO:000641714 | Breast | IDC | regulation of translation | 74/1434 | 468/18723 | 1.67e-09 | 1.53e-07 | 74 |
| GO:004572714 | Breast | IDC | positive regulation of translation | 33/1434 | 136/18723 | 1.92e-09 | 1.73e-07 | 33 |
| GO:003425014 | Breast | IDC | positive regulation of cellular amide metabolic process | 35/1434 | 162/18723 | 1.63e-08 | 1.16e-06 | 35 |
| GO:000218124 | Breast | DCIS | cytoplasmic translation | 82/1390 | 148/18723 | 2.21e-53 | 1.25e-49 | 82 |
| GO:000641724 | Breast | DCIS | regulation of translation | 72/1390 | 468/18723 | 2.46e-09 | 2.17e-07 | 72 |
| GO:004572724 | Breast | DCIS | positive regulation of translation | 32/1390 | 136/18723 | 3.56e-09 | 3.10e-07 | 32 |
| GO:003425023 | Breast | DCIS | positive regulation of cellular amide metabolic process | 34/1390 | 162/18723 | 2.60e-08 | 1.73e-06 | 34 |
| GO:000218110 | Cervix | CC | cytoplasmic translation | 96/2311 | 148/18723 | 4.87e-51 | 2.91e-47 | 96 |
| GO:003425010 | Cervix | CC | positive regulation of cellular amide metabolic process | 40/2311 | 162/18723 | 1.11e-05 | 2.41e-04 | 40 |
| GO:000641710 | Cervix | CC | regulation of translation | 89/2311 | 468/18723 | 1.86e-05 | 3.46e-04 | 89 |
| GO:004572710 | Cervix | CC | positive regulation of translation | 33/2311 | 136/18723 | 9.09e-05 | 1.20e-03 | 33 |
| GO:000218115 | Cervix | HSIL_HPV | cytoplasmic translation | 86/737 | 148/18723 | 3.97e-82 | 1.91e-78 | 86 |
| GO:000641715 | Cervix | HSIL_HPV | regulation of translation | 34/737 | 468/18723 | 4.66e-04 | 6.83e-03 | 34 |
| GO:000218125 | Cervix | N_HPV | cytoplasmic translation | 42/534 | 148/18723 | 2.61e-30 | 1.19e-26 | 42 |
| GO:000641725 | Cervix | N_HPV | regulation of translation | 26/534 | 468/18723 | 9.95e-04 | 1.18e-02 | 26 |
| Page: 1 2 3 4 5 6 7 8 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0301018 | Breast | Precancer | Ribosome | 80/684 | 167/8465 | 7.33e-44 | 2.32e-41 | 1.77e-41 | 80 |
| hsa0517118 | Breast | Precancer | Coronavirus disease - COVID-19 | 81/684 | 232/8465 | 3.74e-32 | 2.36e-30 | 1.81e-30 | 81 |
| hsa0301019 | Breast | Precancer | Ribosome | 80/684 | 167/8465 | 7.33e-44 | 2.32e-41 | 1.77e-41 | 80 |
| hsa0517119 | Breast | Precancer | Coronavirus disease - COVID-19 | 81/684 | 232/8465 | 3.74e-32 | 2.36e-30 | 1.81e-30 | 81 |
| hsa0301024 | Breast | IDC | Ribosome | 83/867 | 167/8465 | 6.07e-39 | 9.87e-37 | 7.38e-37 | 83 |
| hsa0517124 | Breast | IDC | Coronavirus disease - COVID-19 | 86/867 | 232/8465 | 1.50e-28 | 9.72e-27 | 7.27e-27 | 86 |
| hsa0301034 | Breast | IDC | Ribosome | 83/867 | 167/8465 | 6.07e-39 | 9.87e-37 | 7.38e-37 | 83 |
| hsa0517134 | Breast | IDC | Coronavirus disease - COVID-19 | 86/867 | 232/8465 | 1.50e-28 | 9.72e-27 | 7.27e-27 | 86 |
| hsa0301044 | Breast | DCIS | Ribosome | 82/846 | 167/8465 | 8.69e-39 | 1.40e-36 | 1.03e-36 | 82 |
| hsa0517144 | Breast | DCIS | Coronavirus disease - COVID-19 | 86/846 | 232/8465 | 2.42e-29 | 1.56e-27 | 1.15e-27 | 86 |
| hsa0301054 | Breast | DCIS | Ribosome | 82/846 | 167/8465 | 8.69e-39 | 1.40e-36 | 1.03e-36 | 82 |
| hsa0517154 | Breast | DCIS | Coronavirus disease - COVID-19 | 86/846 | 232/8465 | 2.42e-29 | 1.56e-27 | 1.15e-27 | 86 |
| hsa0517120 | Cervix | CC | Coronavirus disease - COVID-19 | 111/1267 | 232/8465 | 1.82e-33 | 5.90e-31 | 3.49e-31 | 111 |
| hsa0301020 | Cervix | CC | Ribosome | 85/1267 | 167/8465 | 3.17e-28 | 5.14e-26 | 3.04e-26 | 85 |
| hsa05171110 | Cervix | CC | Coronavirus disease - COVID-19 | 111/1267 | 232/8465 | 1.82e-33 | 5.90e-31 | 3.49e-31 | 111 |
| hsa03010110 | Cervix | CC | Ribosome | 85/1267 | 167/8465 | 3.17e-28 | 5.14e-26 | 3.04e-26 | 85 |
| hsa0301025 | Cervix | HSIL_HPV | Ribosome | 80/459 | 167/8465 | 9.61e-58 | 2.82e-55 | 2.28e-55 | 80 |
| hsa0517125 | Cervix | HSIL_HPV | Coronavirus disease - COVID-19 | 91/459 | 232/8465 | 2.14e-56 | 3.13e-54 | 2.53e-54 | 91 |
| hsa0301035 | Cervix | HSIL_HPV | Ribosome | 80/459 | 167/8465 | 9.61e-58 | 2.82e-55 | 2.28e-55 | 80 |
| hsa0517135 | Cervix | HSIL_HPV | Coronavirus disease - COVID-19 | 91/459 | 232/8465 | 2.14e-56 | 3.13e-54 | 2.53e-54 | 91 |
| Page: 1 2 3 4 5 6 7 8 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| RPS4X | SNV | Missense_Mutation | c.670N>C | p.Asn224His | p.N224H | P62701 | protein_coding | deleterious(0.01) | benign(0.369) | TCGA-BH-A0HW-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| RPS4X | SNV | Missense_Mutation | c.306N>G | p.Ile102Met | p.I102M | P62701 | protein_coding | tolerated(0.14) | benign(0.206) | TCGA-D8-A1XM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPS4X | SNV | Missense_Mutation | c.88N>T | p.Arg30Cys | p.R30C | P62701 | protein_coding | tolerated(0.16) | benign(0.12) | TCGA-C5-A1BK-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPS4X | SNV | Missense_Mutation | c.235G>A | p.Asp79Asn | p.D79N | P62701 | protein_coding | deleterious(0.05) | benign(0.289) | TCGA-EK-A3GM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RPS4X | SNV | Missense_Mutation | c.161A>G | p.Tyr54Cys | p.Y54C | P62701 | protein_coding | deleterious(0.05) | benign(0.229) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RPS4X | SNV | Missense_Mutation | rs748321540 | c.770C>T | p.Ala257Val | p.A257V | P62701 | protein_coding | tolerated(0.19) | benign(0.046) | TCGA-G4-6302-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPS4X | SNV | Missense_Mutation | c.619G>A | p.Val207Met | p.V207M | P62701 | protein_coding | tolerated(0.21) | benign(0.107) | TCGA-AG-A025-01 | Colorectum | rectum adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| RPS4X | SNV | Missense_Mutation | novel | c.443N>A | p.Arg148His | p.R148H | P62701 | protein_coding | tolerated(0.12) | benign(0.125) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
| RPS4X | SNV | Missense_Mutation | novel | c.298N>T | p.Arg100Cys | p.R100C | P62701 | protein_coding | tolerated(0.13) | benign(0.014) | TCGA-AJ-A3EL-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS4X | SNV | Missense_Mutation | c.734N>A | p.Arg245His | p.R245H | P62701 | protein_coding | tolerated(0.32) | benign(0.007) | TCGA-AX-A06F-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | carboplatin | SD |
| Page: 1 2 |
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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 |
| Page: 1 |
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