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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 | RNA-P7T1-P7T1-1 | Human | Lung | AIS | 3.80e-10 | -2.87e-01 | -0.0961 |
6191 | RPS4X | RNA-P7T1-P7T1-2 | Human | Lung | AIS | 1.23e-10 | -2.98e-01 | -0.0876 |
6191 | RPS4X | RNA-P7T1-P7T1-3 | Human | Lung | AIS | 2.64e-12 | -4.21e-01 | -0.0822 |
6191 | RPS4X | RNA-P7T1-P7T1-4 | Human | Lung | AIS | 3.41e-16 | -2.74e-01 | -0.0809 |
6191 | RPS4X | RNA-P8T2-P8T2-3 | Human | Lung | AIS | 5.90e-07 | -6.49e-01 | -0.1284 |
6191 | RPS4X | C04 | Human | Oral cavity | OSCC | 1.10e-90 | 4.42e+00 | 0.2633 |
6191 | RPS4X | C21 | Human | Oral cavity | OSCC | 1.45e-84 | 4.47e+00 | 0.2678 |
6191 | RPS4X | C30 | Human | Oral cavity | OSCC | 5.18e-110 | 5.21e+00 | 0.3055 |
6191 | RPS4X | C38 | Human | Oral cavity | OSCC | 2.91e-77 | 4.76e+00 | 0.172 |
6191 | RPS4X | C43 | Human | Oral cavity | OSCC | 5.60e-119 | 5.47e+00 | 0.1704 |
6191 | RPS4X | C46 | Human | Oral cavity | OSCC | 5.16e-67 | 4.02e+00 | 0.1673 |
6191 | RPS4X | C51 | Human | Oral cavity | OSCC | 2.06e-73 | 3.78e+00 | 0.2674 |
6191 | RPS4X | C57 | Human | Oral cavity | OSCC | 1.49e-36 | 2.76e+00 | 0.1679 |
6191 | RPS4X | C06 | Human | Oral cavity | OSCC | 8.65e-86 | 4.41e+00 | 0.2699 |
6191 | RPS4X | C07 | Human | Oral cavity | OSCC | 9.92e-54 | 3.97e+00 | 0.2491 |
6191 | RPS4X | C08 | Human | Oral cavity | OSCC | 2.41e-100 | 4.70e+00 | 0.1919 |
6191 | RPS4X | C86 | Human | Oral cavity | OSCC | 2.21e-36 | 3.18e+00 | 0.161 |
6191 | RPS4X | C09 | Human | Oral cavity | OSCC | 4.38e-50 | 4.18e+00 | 0.1431 |
6191 | RPS4X | LN22 | Human | Oral cavity | OSCC | 1.55e-75 | 3.61e+00 | 0.1733 |
6191 | RPS4X | LN38 | Human | Oral cavity | OSCC | 3.99e-82 | 4.44e+00 | 0.168 |
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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: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 |
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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 |
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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 |
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 |
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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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