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Gene: RPSA |
Gene summary for RPSA |
Gene summary. |
Gene information | Species | Human | Gene symbol | RPSA | Gene ID | 3921 |
Gene name | ribosomal protein SA | |
Gene Alias | 37LRP | |
Cytomap | 3p22.1 | |
Gene Type | protein-coding | GO ID | GO:0000028 | UniProtAcc | A0A0C4DG17 |
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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 |
3921 | RPSA | T3 | Human | Cervix | CC | 1.05e-77 | -6.12e-01 | 0.1389 |
3921 | RPSA | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.56e-64 | 1.54e+00 | 0.0155 |
3921 | RPSA | HTA11_2487_2000001011 | Human | Colorectum | SER | 2.01e-37 | 2.23e+00 | -0.1808 |
3921 | RPSA | HTA11_2951_2000001011 | Human | Colorectum | AD | 2.74e-29 | 2.33e+00 | 0.0216 |
3921 | RPSA | HTA11_1938_2000001011 | Human | Colorectum | AD | 5.44e-46 | 2.22e+00 | -0.0811 |
3921 | RPSA | HTA11_78_2000001011 | Human | Colorectum | AD | 1.04e-33 | 1.51e+00 | -0.1088 |
3921 | RPSA | HTA11_347_2000001011 | Human | Colorectum | AD | 5.96e-57 | 2.29e+00 | -0.1954 |
3921 | RPSA | HTA11_411_2000001011 | Human | Colorectum | SER | 1.90e-20 | 2.29e+00 | -0.2602 |
3921 | RPSA | HTA11_2112_2000001011 | Human | Colorectum | SER | 2.37e-09 | 2.15e+00 | -0.2196 |
3921 | RPSA | HTA11_3361_2000001011 | Human | Colorectum | AD | 7.90e-34 | 2.11e+00 | -0.1207 |
3921 | RPSA | HTA11_83_2000001011 | Human | Colorectum | SER | 4.38e-35 | 2.09e+00 | -0.1526 |
3921 | RPSA | HTA11_696_2000001011 | Human | Colorectum | AD | 2.77e-77 | 2.52e+00 | -0.1464 |
3921 | RPSA | HTA11_866_2000001011 | Human | Colorectum | AD | 1.19e-50 | 1.91e+00 | -0.1001 |
3921 | RPSA | HTA11_1391_2000001011 | Human | Colorectum | AD | 2.61e-60 | 2.83e+00 | -0.059 |
3921 | RPSA | HTA11_2992_2000001011 | Human | Colorectum | SER | 2.90e-20 | 1.96e+00 | -0.1706 |
3921 | RPSA | HTA11_5212_2000001011 | Human | Colorectum | AD | 1.76e-08 | 1.39e+00 | -0.2061 |
3921 | RPSA | HTA11_5216_2000001011 | Human | Colorectum | SER | 2.39e-16 | 1.92e+00 | -0.1462 |
3921 | RPSA | HTA11_546_2000001011 | Human | Colorectum | AD | 9.66e-37 | 2.57e+00 | -0.0842 |
3921 | RPSA | HTA11_9341_2000001011 | Human | Colorectum | SER | 2.18e-13 | 1.94e+00 | -0.00410000000000005 |
3921 | RPSA | HTA11_7862_2000001011 | Human | Colorectum | AD | 7.99e-38 | 2.04e+00 | -0.0179 |
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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:00226139 | Breast | Precancer | ribonucleoprotein complex biogenesis | 79/1080 | 463/18723 | 2.11e-18 | 1.03e-15 | 79 |
GO:00718269 | Breast | Precancer | ribonucleoprotein complex subunit organization | 48/1080 | 227/18723 | 2.68e-15 | 8.45e-13 | 48 |
GO:00226189 | Breast | Precancer | ribonucleoprotein complex assembly | 47/1080 | 220/18723 | 3.47e-15 | 1.03e-12 | 47 |
GO:00422549 | Breast | Precancer | ribosome biogenesis | 52/1080 | 299/18723 | 7.35e-13 | 1.51e-10 | 52 |
GO:00422559 | Breast | Precancer | ribosome assembly | 21/1080 | 61/18723 | 1.06e-11 | 1.53e-09 | 21 |
GO:00160329 | Breast | Precancer | viral process | 58/1080 | 415/18723 | 3.42e-10 | 3.16e-08 | 58 |
GO:00422749 | Breast | Precancer | ribosomal small subunit biogenesis | 21/1080 | 73/18723 | 4.84e-10 | 4.39e-08 | 21 |
GO:00190589 | Breast | Precancer | viral life cycle | 47/1080 | 317/18723 | 2.42e-09 | 1.99e-07 | 47 |
GO:00000289 | Breast | Precancer | ribosomal small subunit assembly | 10/1080 | 19/18723 | 2.24e-08 | 1.50e-06 | 10 |
GO:00444039 | Breast | Precancer | biological process involved in symbiotic interaction | 42/1080 | 290/18723 | 3.40e-08 | 2.11e-06 | 42 |
GO:00521269 | Breast | Precancer | movement in host environment | 29/1080 | 175/18723 | 2.59e-07 | 1.28e-05 | 29 |
GO:00517019 | Breast | Precancer | biological process involved in interaction with host | 31/1080 | 203/18723 | 6.52e-07 | 2.71e-05 | 31 |
GO:00444099 | Breast | Precancer | entry into host | 25/1080 | 151/18723 | 1.74e-06 | 6.19e-05 | 25 |
GO:00467189 | Breast | Precancer | viral entry into host cell | 24/1080 | 144/18723 | 2.46e-06 | 8.35e-05 | 24 |
GO:000218114 | Breast | IDC | cytoplasmic translation | 82/1434 | 148/18723 | 2.60e-52 | 1.48e-48 | 82 |
GO:002261314 | Breast | IDC | ribonucleoprotein complex biogenesis | 83/1434 | 463/18723 | 2.01e-13 | 5.20e-11 | 83 |
GO:007182614 | Breast | IDC | ribonucleoprotein complex subunit organization | 52/1434 | 227/18723 | 5.18e-13 | 1.21e-10 | 52 |
GO:002261814 | Breast | IDC | ribonucleoprotein complex assembly | 51/1434 | 220/18723 | 5.32e-13 | 1.21e-10 | 51 |
GO:001603214 | Breast | IDC | viral process | 75/1434 | 415/18723 | 1.98e-12 | 4.02e-10 | 75 |
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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 |
RPSA | SNV | Missense_Mutation | novel | c.774G>T | p.Gln258His | p.Q258H | protein_coding | deleterious(0.01) | possibly_damaging(0.866) | TCGA-5M-AAT6-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | PD | |
RPSA | SNV | Missense_Mutation | novel | c.797N>G | p.Gln266Arg | p.Q266R | protein_coding | deleterious(0.03) | benign(0.019) | TCGA-AA-3984-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
RPSA | SNV | Missense_Mutation | rs771423193 | c.566N>A | p.Arg189His | p.R189H | protein_coding | tolerated(0.33) | benign(0.007) | TCGA-WS-AB45-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
RPSA | SNV | Missense_Mutation | novel | c.774N>T | p.Gln258His | p.Q258H | protein_coding | deleterious(0.01) | possibly_damaging(0.866) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RPSA | SNV | Missense_Mutation | novel | c.774N>T | p.Gln258His | p.Q258H | protein_coding | deleterious(0.01) | possibly_damaging(0.866) | TCGA-A5-A0GG-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RPSA | SNV | Missense_Mutation | novel | c.80G>A | p.Gly27Asp | p.G27D | protein_coding | tolerated(0.12) | benign(0.139) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
RPSA | SNV | Missense_Mutation | novel | c.575N>A | p.Gly192Asp | p.G192D | protein_coding | deleterious(0.04) | benign(0.088) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
RPSA | SNV | Missense_Mutation | c.690G>T | p.Glu230Asp | p.E230D | protein_coding | tolerated(0.08) | benign(0.159) | TCGA-B5-A11E-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
RPSA | SNV | Missense_Mutation | novel | c.221N>C | p.Val74Ala | p.V74A | protein_coding | deleterious(0.01) | probably_damaging(0.98) | TCGA-EO-A3B0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
RPSA | SNV | Missense_Mutation | novel | c.127A>C | p.Ser43Arg | p.S43R | protein_coding | deleterious(0.04) | benign(0.154) | TCGA-QF-A5YS-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
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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 |
3921 | RPSA | NA | PMID25747044-Compound-miRNA | |||
3921 | RPSA | NA | MITOXANTRONE | MITOXANTRONE | 8630412 | |
3921 | RPSA | NA | DOXORUBICIN | DOXORUBICIN | 11493465 | |
3921 | RPSA | NA | DAUNORUBICIN | DAUNORUBICIN | 15161018 |
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