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Gene: RPS3 |
Gene summary for RPS3 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RPS3 | Gene ID | 6188 |
Gene name | ribosomal protein S3 | |
Gene Alias | S3 | |
Cytomap | 11q13.4 | |
Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | P23396 |
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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 |
6188 | RPS3 | GSM4909281 | Human | Breast | IDC | 5.13e-05 | -1.06e-01 | 0.21 |
6188 | RPS3 | GSM4909286 | Human | Breast | IDC | 1.63e-66 | 2.87e-01 | 0.1081 |
6188 | RPS3 | GSM4909287 | Human | Breast | IDC | 6.06e-10 | -2.29e-01 | 0.2057 |
6188 | RPS3 | GSM4909293 | Human | Breast | IDC | 4.84e-48 | -2.61e-01 | 0.1581 |
6188 | RPS3 | GSM4909294 | Human | Breast | IDC | 2.76e-15 | -2.22e-01 | 0.2022 |
6188 | RPS3 | GSM4909296 | Human | Breast | IDC | 7.26e-14 | 1.56e-01 | 0.1524 |
6188 | RPS3 | GSM4909297 | Human | Breast | IDC | 8.12e-46 | -5.16e-01 | 0.1517 |
6188 | RPS3 | GSM4909298 | Human | Breast | IDC | 8.34e-59 | -3.56e-01 | 0.1551 |
6188 | RPS3 | GSM4909301 | Human | Breast | IDC | 3.09e-16 | -1.73e-01 | 0.1577 |
6188 | RPS3 | GSM4909306 | Human | Breast | IDC | 2.66e-12 | -1.55e-01 | 0.1564 |
6188 | RPS3 | GSM4909311 | Human | Breast | IDC | 1.05e-03 | -6.27e-02 | 0.1534 |
6188 | RPS3 | GSM4909312 | Human | Breast | IDC | 2.11e-15 | 1.66e-01 | 0.1552 |
6188 | RPS3 | GSM4909313 | Human | Breast | IDC | 1.58e-04 | 9.27e-02 | 0.0391 |
6188 | RPS3 | GSM4909315 | Human | Breast | IDC | 1.77e-14 | -2.18e-01 | 0.21 |
6188 | RPS3 | GSM4909317 | Human | Breast | IDC | 8.23e-26 | -3.20e-01 | 0.1355 |
6188 | RPS3 | GSM4909319 | Human | Breast | IDC | 4.80e-27 | -4.81e-01 | 0.1563 |
6188 | RPS3 | brca2 | Human | Breast | Precancer | 2.55e-20 | -1.71e-01 | -0.024 |
6188 | RPS3 | M1 | Human | Breast | IDC | 1.22e-04 | -1.44e-01 | 0.1577 |
6188 | RPS3 | NCCBC14 | Human | Breast | DCIS | 3.56e-14 | -3.83e-01 | 0.2021 |
6188 | RPS3 | NCCBC5 | Human | Breast | DCIS | 2.91e-04 | -2.31e-01 | 0.2046 |
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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:00971939 | Breast | Precancer | intrinsic apoptotic signaling pathway | 59/1080 | 288/18723 | 8.07e-18 | 3.60e-15 | 59 |
GO:20012339 | Breast | Precancer | regulation of apoptotic signaling pathway | 65/1080 | 356/18723 | 7.70e-17 | 3.17e-14 | 65 |
GO:20012429 | Breast | Precancer | regulation of intrinsic apoptotic signaling pathway | 41/1080 | 164/18723 | 6.48e-16 | 2.31e-13 | 41 |
GO:00069799 | Breast | Precancer | response to oxidative stress | 70/1080 | 446/18723 | 1.59e-14 | 4.26e-12 | 70 |
GO:00525479 | Breast | Precancer | regulation of peptidase activity | 71/1080 | 461/18723 | 2.72e-14 | 6.94e-12 | 71 |
GO:00525489 | Breast | Precancer | regulation of endopeptidase activity | 67/1080 | 432/18723 | 1.06e-13 | 2.36e-11 | 67 |
GO:00064138 | Breast | Precancer | translational initiation | 30/1080 | 118/18723 | 3.23e-12 | 5.58e-10 | 30 |
GO:00064179 | Breast | Precancer | regulation of translation | 67/1080 | 468/18723 | 4.71e-12 | 7.64e-10 | 67 |
GO:20001169 | Breast | Precancer | regulation of cysteine-type endopeptidase activity | 43/1080 | 235/18723 | 1.30e-11 | 1.83e-09 | 43 |
GO:00432819 | Breast | Precancer | regulation of cysteine-type endopeptidase activity involved in apoptotic process | 40/1080 | 209/18723 | 1.59e-11 | 2.07e-09 | 40 |
GO:00621979 | Breast | Precancer | cellular response to chemical stress | 51/1080 | 337/18723 | 2.40e-10 | 2.34e-08 | 51 |
GO:00003029 | Breast | Precancer | response to reactive oxygen species | 38/1080 | 222/18723 | 1.47e-09 | 1.23e-07 | 38 |
GO:00458629 | Breast | Precancer | positive regulation of proteolysis | 51/1080 | 372/18723 | 7.77e-09 | 5.70e-07 | 51 |
GO:20012445 | Breast | Precancer | positive regulation of intrinsic apoptotic signaling pathway | 17/1080 | 58/18723 | 1.59e-08 | 1.12e-06 | 17 |
GO:19033209 | Breast | Precancer | regulation of protein modification by small protein conjugation or removal | 38/1080 | 242/18723 | 1.71e-08 | 1.17e-06 | 38 |
GO:00345999 | Breast | Precancer | cellular response to oxidative stress | 42/1080 | 288/18723 | 2.78e-08 | 1.79e-06 | 42 |
GO:00109529 | Breast | Precancer | positive regulation of peptidase activity | 33/1080 | 197/18723 | 3.01e-08 | 1.89e-06 | 33 |
GO:19033219 | Breast | Precancer | negative regulation of protein modification by small protein conjugation or removal | 21/1080 | 95/18723 | 8.09e-08 | 4.61e-06 | 21 |
GO:00313969 | Breast | Precancer | regulation of protein ubiquitination | 33/1080 | 210/18723 | 1.45e-07 | 7.82e-06 | 33 |
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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 |
hsa0513218 | Breast | Precancer | Salmonella infection | 49/684 | 249/8465 | 2.92e-09 | 6.15e-08 | 4.71e-08 | 49 |
hsa0513018 | Breast | Precancer | Pathogenic Escherichia coli infection | 38/684 | 197/8465 | 3.12e-07 | 5.81e-06 | 4.45e-06 | 38 |
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 |
hsa0513219 | Breast | Precancer | Salmonella infection | 49/684 | 249/8465 | 2.92e-09 | 6.15e-08 | 4.71e-08 | 49 |
hsa0513019 | Breast | Precancer | Pathogenic Escherichia coli infection | 38/684 | 197/8465 | 3.12e-07 | 5.81e-06 | 4.45e-06 | 38 |
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 |
hsa0513224 | Breast | IDC | Salmonella infection | 55/867 | 249/8465 | 2.07e-08 | 4.49e-07 | 3.36e-07 | 55 |
hsa0513024 | Breast | IDC | Pathogenic Escherichia coli infection | 42/867 | 197/8465 | 2.66e-06 | 3.92e-05 | 2.94e-05 | 42 |
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 |
hsa0513234 | Breast | IDC | Salmonella infection | 55/867 | 249/8465 | 2.07e-08 | 4.49e-07 | 3.36e-07 | 55 |
hsa0513034 | Breast | IDC | Pathogenic Escherichia coli infection | 42/867 | 197/8465 | 2.66e-06 | 3.92e-05 | 2.94e-05 | 42 |
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 |
hsa0513243 | Breast | DCIS | Salmonella infection | 55/846 | 249/8465 | 8.71e-09 | 1.87e-07 | 1.38e-07 | 55 |
hsa0513043 | Breast | DCIS | Pathogenic Escherichia coli infection | 42/846 | 197/8465 | 1.40e-06 | 2.15e-05 | 1.59e-05 | 42 |
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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 |
RPS3 | SNV | Missense_Mutation | c.212N>A | p.Ala71Asp | p.A71D | P23396 | protein_coding | deleterious(0.01) | possibly_damaging(0.786) | TCGA-AA-3672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
RPS3 | SNV | Missense_Mutation | rs1802703 | c.376N>A | p.Leu126Ile | p.L126I | P23396 | protein_coding | tolerated(0.16) | benign(0.045) | TCGA-AD-6889-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | xeloda | PD |
RPS3 | SNV | Missense_Mutation | c.43N>C | p.Gly15Arg | p.G15R | P23396 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AG-A02X-01 | Colorectum | rectum adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
RPS3 | SNV | Missense_Mutation | c.419N>A | p.Arg140Gln | p.R140Q | P23396 | protein_coding | tolerated(0.1) | possibly_damaging(0.855) | TCGA-EF-5830-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
RPS3 | SNV | Missense_Mutation | c.89N>A | p.Ala30Asp | p.A30D | P23396 | protein_coding | deleterious(0.01) | probably_damaging(0.924) | TCGA-AX-A06D-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Chemotherapy | carboplatin | PD | |
RPS3 | SNV | Missense_Mutation | c.89C>A | p.Ala30Asp | p.A30D | P23396 | protein_coding | deleterious(0.01) | probably_damaging(0.924) | TCGA-AX-A06H-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | SD | |
RPS3 | SNV | Missense_Mutation | rs747317928 | c.565N>T | p.Arg189Cys | p.R189C | P23396 | protein_coding | tolerated(0.12) | probably_damaging(1) | TCGA-B5-A11J-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RPS3 | SNV | Missense_Mutation | c.664N>A | p.Asp222Asn | p.D222N | P23396 | protein_coding | deleterious(0.03) | benign(0.278) | TCGA-D1-A160-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
RPS3 | SNV | Missense_Mutation | novel | c.655C>T | p.Pro219Ser | p.P219S | P23396 | protein_coding | tolerated(0.1) | possibly_damaging(0.767) | TCGA-D1-A175-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | paclitaxel | SD |
RPS3 | SNV | Missense_Mutation | c.85N>A | p.Leu29Met | p.L29M | P23396 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-DF-A2KU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | 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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