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Gene: RPS19 |
Gene summary for RPS19 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RPS19 | Gene ID | 6223 |
Gene name | ribosomal protein S19 | |
Gene Alias | DBA | |
Cytomap | 19q13.2 | |
Gene Type | protein-coding | GO ID | GO:0000028 | UniProtAcc | B0ZBD0 |
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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 |
6223 | RPS19 | GSM4909282 | Human | Breast | IDC | 1.18e-40 | -2.16e-01 | -0.0288 |
6223 | RPS19 | GSM4909286 | Human | Breast | IDC | 2.89e-43 | 2.01e-01 | 0.1081 |
6223 | RPS19 | GSM4909287 | Human | Breast | IDC | 1.80e-11 | -1.82e-01 | 0.2057 |
6223 | RPS19 | GSM4909293 | Human | Breast | IDC | 1.12e-51 | -2.45e-01 | 0.1581 |
6223 | RPS19 | GSM4909294 | Human | Breast | IDC | 1.44e-45 | -3.14e-01 | 0.2022 |
6223 | RPS19 | GSM4909296 | Human | Breast | IDC | 3.14e-09 | 1.08e-01 | 0.1524 |
6223 | RPS19 | GSM4909297 | Human | Breast | IDC | 2.49e-16 | -1.70e-01 | 0.1517 |
6223 | RPS19 | GSM4909298 | Human | Breast | IDC | 2.09e-30 | -1.74e-01 | 0.1551 |
6223 | RPS19 | GSM4909301 | Human | Breast | IDC | 1.27e-05 | -9.85e-02 | 0.1577 |
6223 | RPS19 | GSM4909304 | Human | Breast | IDC | 6.16e-19 | -1.30e-01 | 0.1636 |
6223 | RPS19 | GSM4909307 | Human | Breast | IDC | 5.19e-03 | -6.81e-02 | 0.1569 |
6223 | RPS19 | GSM4909308 | Human | Breast | IDC | 1.78e-16 | -1.83e-01 | 0.158 |
6223 | RPS19 | GSM4909311 | Human | Breast | IDC | 4.17e-03 | 7.44e-02 | 0.1534 |
6223 | RPS19 | GSM4909315 | Human | Breast | IDC | 1.22e-14 | -1.63e-01 | 0.21 |
6223 | RPS19 | GSM4909316 | Human | Breast | IDC | 1.69e-06 | -3.05e-01 | 0.21 |
6223 | RPS19 | GSM4909317 | Human | Breast | IDC | 1.42e-19 | -2.38e-01 | 0.1355 |
6223 | RPS19 | GSM4909318 | Human | Breast | IDC | 3.18e-03 | -3.07e-01 | 0.2031 |
6223 | RPS19 | GSM4909319 | Human | Breast | IDC | 8.88e-89 | -9.24e-01 | 0.1563 |
6223 | RPS19 | brca2 | Human | Breast | Precancer | 7.82e-33 | -1.96e-01 | -0.024 |
6223 | RPS19 | brca3 | Human | Breast | Precancer | 3.49e-14 | -1.24e-01 | -0.0263 |
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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:0045824 | Colorectum | MSI-H | negative regulation of innate immune response | 13/1319 | 71/18723 | 1.24e-03 | 2.00e-02 | 13 |
GO:00457301 | Colorectum | MSI-H | respiratory burst | 8/1319 | 37/18723 | 3.64e-03 | 4.28e-02 | 8 |
GO:00021814 | Colorectum | FAP | cytoplasmic translation | 76/2622 | 148/18723 | 3.31e-27 | 2.03e-23 | 76 |
GO:00718264 | Colorectum | FAP | ribonucleoprotein complex subunit organization | 59/2622 | 227/18723 | 1.18e-06 | 5.26e-05 | 59 |
GO:00226184 | Colorectum | FAP | ribonucleoprotein complex assembly | 57/2622 | 220/18723 | 1.99e-06 | 8.03e-05 | 57 |
GO:00341014 | Colorectum | FAP | erythrocyte homeostasis | 37/2622 | 129/18723 | 1.06e-05 | 3.01e-04 | 37 |
GO:00302184 | Colorectum | FAP | erythrocyte differentiation | 34/2622 | 120/18723 | 3.13e-05 | 7.11e-04 | 34 |
GO:00300994 | Colorectum | FAP | myeloid cell differentiation | 81/2622 | 381/18723 | 6.33e-05 | 1.22e-03 | 81 |
GO:00488724 | Colorectum | FAP | homeostasis of number of cells | 60/2622 | 272/18723 | 1.91e-04 | 2.79e-03 | 60 |
GO:00022624 | Colorectum | FAP | myeloid cell homeostasis | 39/2622 | 157/18723 | 2.03e-04 | 2.92e-03 | 39 |
GO:00226134 | Colorectum | FAP | ribonucleoprotein complex biogenesis | 91/2622 | 463/18723 | 4.28e-04 | 5.12e-03 | 91 |
GO:00000284 | Colorectum | FAP | ribosomal small subunit assembly | 8/2622 | 19/18723 | 2.61e-03 | 2.03e-02 | 8 |
GO:00422554 | Colorectum | FAP | ribosome assembly | 17/2622 | 61/18723 | 3.43e-03 | 2.48e-02 | 17 |
GO:00021815 | Colorectum | CRC | cytoplasmic translation | 70/2078 | 148/18723 | 1.53e-28 | 9.16e-25 | 70 |
GO:00226185 | Colorectum | CRC | ribonucleoprotein complex assembly | 48/2078 | 220/18723 | 3.16e-06 | 1.44e-04 | 48 |
GO:00718265 | Colorectum | CRC | ribonucleoprotein complex subunit organization | 49/2078 | 227/18723 | 3.44e-06 | 1.51e-04 | 49 |
GO:00000285 | Colorectum | CRC | ribosomal small subunit assembly | 10/2078 | 19/18723 | 9.95e-06 | 3.31e-04 | 10 |
GO:00341015 | Colorectum | CRC | erythrocyte homeostasis | 30/2078 | 129/18723 | 6.14e-05 | 1.35e-03 | 30 |
GO:00422555 | Colorectum | CRC | ribosome assembly | 18/2078 | 61/18723 | 7.27e-05 | 1.53e-03 | 18 |
GO:00300995 | Colorectum | CRC | myeloid cell differentiation | 66/2078 | 381/18723 | 1.59e-04 | 2.87e-03 | 66 |
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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 |
RPS19 | SNV | Missense_Mutation | c.52N>G | p.Leu18Val | p.L18V | P39019 | protein_coding | tolerated(0.13) | benign(0.158) | TCGA-DS-A1OC-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | gemcitabine | SD | |
RPS19 | SNV | Missense_Mutation | c.52N>G | p.Leu18Val | p.L18V | P39019 | protein_coding | tolerated(0.13) | benign(0.158) | TCGA-JX-A3Q0-01 | Cervix | cervical & endocervical cancer | Female | <65 | III/IV | Unknown | Unknown | SD | |
RPS19 | SNV | Missense_Mutation | c.305N>T | p.Arg102Leu | p.R102L | P39019 | protein_coding | tolerated(0.08) | benign(0.006) | TCGA-VS-A94Z-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
RPS19 | SNV | Missense_Mutation | novel | c.150N>T | p.Glu50Asp | p.E50D | P39019 | protein_coding | tolerated(0.24) | benign(0.005) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
RPS19 | SNV | Missense_Mutation | novel | c.80N>C | p.Lys27Thr | p.K27T | P39019 | protein_coding | deleterious(0) | probably_damaging(0.981) | TCGA-EO-A22R-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
RPS19 | SNV | Missense_Mutation | novel | c.404N>G | p.Ala135Gly | p.A135G | P39019 | protein_coding | deleterious(0) | possibly_damaging(0.897) | TCGA-QS-A8F1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Chemotherapy | carboplatin | PD |
RPS19 | SNV | Missense_Mutation | c.209C>T | p.Ala70Val | p.A70V | P39019 | protein_coding | tolerated(1) | benign(0.019) | TCGA-50-5946-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | PD | |
RPS19 | SNV | Missense_Mutation | c.302N>A | p.Arg101His | p.R101H | P39019 | protein_coding | tolerated(0.07) | benign(0.172) | TCGA-CN-4728-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | vectibix | 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 |
6223 | RPS19 | NA | VITAMIN A | 12175513 | ||
6223 | RPS19 | NA | DEXAMETHASONE | DEXAMETHASONE | 15755903 |
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