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Gene: RPS6KA4 |
Gene summary for RPS6KA4 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RPS6KA4 | Gene ID | 8986 |
| Gene name | ribosomal protein S6 kinase A4 | |
| Gene Alias | MSK2 | |
| Cytomap | 11q13.1 | |
| Gene Type | protein-coding | GO ID | GO:0001816 | UniProtAcc | O75676 |
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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 |
| 8986 | RPS6KA4 | LZE7T | Human | Esophagus | ESCC | 5.25e-03 | 1.71e-01 | 0.0667 |
| 8986 | RPS6KA4 | LZE22T | Human | Esophagus | ESCC | 2.09e-03 | 2.93e-01 | 0.068 |
| 8986 | RPS6KA4 | LZE24T | Human | Esophagus | ESCC | 3.23e-16 | 5.24e-01 | 0.0596 |
| 8986 | RPS6KA4 | P1T-E | Human | Esophagus | ESCC | 1.65e-04 | 2.35e-01 | 0.0875 |
| 8986 | RPS6KA4 | P2T-E | Human | Esophagus | ESCC | 1.20e-09 | 1.91e-01 | 0.1177 |
| 8986 | RPS6KA4 | P4T-E | Human | Esophagus | ESCC | 4.47e-18 | 3.61e-01 | 0.1323 |
| 8986 | RPS6KA4 | P5T-E | Human | Esophagus | ESCC | 1.53e-17 | 3.85e-01 | 0.1327 |
| 8986 | RPS6KA4 | P8T-E | Human | Esophagus | ESCC | 1.45e-13 | 2.53e-01 | 0.0889 |
| 8986 | RPS6KA4 | P9T-E | Human | Esophagus | ESCC | 6.14e-10 | 1.85e-01 | 0.1131 |
| 8986 | RPS6KA4 | P10T-E | Human | Esophagus | ESCC | 9.86e-15 | 1.79e-01 | 0.116 |
| 8986 | RPS6KA4 | P11T-E | Human | Esophagus | ESCC | 1.03e-13 | 5.65e-01 | 0.1426 |
| 8986 | RPS6KA4 | P12T-E | Human | Esophagus | ESCC | 2.61e-17 | 3.88e-01 | 0.1122 |
| 8986 | RPS6KA4 | P15T-E | Human | Esophagus | ESCC | 3.88e-06 | 1.38e-01 | 0.1149 |
| 8986 | RPS6KA4 | P16T-E | Human | Esophagus | ESCC | 4.59e-11 | 9.64e-02 | 0.1153 |
| 8986 | RPS6KA4 | P17T-E | Human | Esophagus | ESCC | 2.46e-14 | 4.79e-01 | 0.1278 |
| 8986 | RPS6KA4 | P19T-E | Human | Esophagus | ESCC | 2.98e-07 | 5.55e-01 | 0.1662 |
| 8986 | RPS6KA4 | P20T-E | Human | Esophagus | ESCC | 9.31e-12 | 2.37e-01 | 0.1124 |
| 8986 | RPS6KA4 | P21T-E | Human | Esophagus | ESCC | 2.30e-43 | 9.35e-01 | 0.1617 |
| 8986 | RPS6KA4 | P22T-E | Human | Esophagus | ESCC | 4.83e-07 | 1.39e-01 | 0.1236 |
| 8986 | RPS6KA4 | P23T-E | Human | Esophagus | ESCC | 1.80e-12 | 3.01e-01 | 0.108 |
| Page: 1 2 3 4 5 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ |
| ∗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:001657015 | Esophagus | ESCC | histone modification | 323/8552 | 463/18723 | 2.61e-26 | 7.88e-24 | 323 |
| GO:001820514 | Esophagus | ESCC | peptidyl-lysine modification | 259/8552 | 376/18723 | 3.90e-20 | 5.26e-18 | 259 |
| GO:001839413 | Esophagus | ESCC | peptidyl-lysine acetylation | 123/8552 | 169/18723 | 6.58e-13 | 2.94e-11 | 123 |
| GO:004354313 | Esophagus | ESCC | protein acylation | 165/8552 | 243/18723 | 1.69e-12 | 7.14e-11 | 165 |
| GO:000647313 | Esophagus | ESCC | protein acetylation | 140/8552 | 201/18723 | 4.37e-12 | 1.69e-10 | 140 |
| GO:001839313 | Esophagus | ESCC | internal peptidyl-lysine acetylation | 114/8552 | 158/18723 | 1.16e-11 | 4.24e-10 | 114 |
| GO:000647513 | Esophagus | ESCC | internal protein amino acid acetylation | 115/8552 | 160/18723 | 1.43e-11 | 5.08e-10 | 115 |
| GO:00165735 | Esophagus | ESCC | histone acetylation | 110/8552 | 152/18723 | 1.95e-11 | 6.81e-10 | 110 |
| GO:003105614 | Esophagus | ESCC | regulation of histone modification | 106/8552 | 152/18723 | 1.52e-09 | 3.55e-08 | 106 |
| GO:00510908 | Esophagus | ESCC | regulation of DNA-binding transcription factor activity | 252/8552 | 440/18723 | 5.22e-07 | 6.97e-06 | 252 |
| GO:00310583 | Esophagus | ESCC | positive regulation of histone modification | 65/8552 | 92/18723 | 1.04e-06 | 1.31e-05 | 65 |
| GO:00182099 | Esophagus | ESCC | peptidyl-serine modification | 196/8552 | 338/18723 | 3.07e-06 | 3.47e-05 | 196 |
| GO:001810515 | Esophagus | ESCC | peptidyl-serine phosphorylation | 184/8552 | 315/18723 | 3.22e-06 | 3.61e-05 | 184 |
| GO:00510918 | Esophagus | ESCC | positive regulation of DNA-binding transcription factor activity | 155/8552 | 260/18723 | 3.83e-06 | 4.14e-05 | 155 |
| GO:20007564 | Esophagus | ESCC | regulation of peptidyl-lysine acetylation | 43/8552 | 63/18723 | 2.43e-04 | 1.50e-03 | 43 |
| GO:00510926 | Esophagus | ESCC | positive regulation of NF-kappaB transcription factor activity | 91/8552 | 152/18723 | 2.91e-04 | 1.75e-03 | 91 |
| GO:19019835 | Esophagus | ESCC | regulation of protein acetylation | 49/8552 | 77/18723 | 1.12e-03 | 5.60e-03 | 49 |
| GO:00350653 | Esophagus | ESCC | regulation of histone acetylation | 36/8552 | 54/18723 | 1.49e-03 | 7.06e-03 | 36 |
| GO:00165721 | Esophagus | ESCC | histone phosphorylation | 27/8552 | 39/18723 | 2.52e-03 | 1.08e-02 | 27 |
| GO:00331271 | Esophagus | ESCC | regulation of histone phosphorylation | 10/8552 | 12/18723 | 8.94e-03 | 3.12e-02 | 10 |
| Page: 1 2 3 4 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0466810 | Esophagus | ESCC | TNF signaling pathway | 89/4205 | 114/8465 | 3.36e-10 | 4.01e-09 | 2.06e-09 | 89 |
| hsa0466817 | Esophagus | ESCC | TNF signaling pathway | 89/4205 | 114/8465 | 3.36e-10 | 4.01e-09 | 2.06e-09 | 89 |
| hsa046689 | Oral cavity | OSCC | TNF signaling pathway | 82/3704 | 114/8465 | 8.30e-10 | 9.59e-09 | 4.88e-09 | 82 |
| hsa0401014 | Oral cavity | OSCC | MAPK signaling pathway | 165/3704 | 302/8465 | 7.11e-05 | 2.74e-04 | 1.40e-04 | 165 |
| hsa0466816 | Oral cavity | OSCC | TNF signaling pathway | 82/3704 | 114/8465 | 8.30e-10 | 9.59e-09 | 4.88e-09 | 82 |
| hsa0401015 | Oral cavity | OSCC | MAPK signaling pathway | 165/3704 | 302/8465 | 7.11e-05 | 2.74e-04 | 1.40e-04 | 165 |
| hsa0466822 | Oral cavity | LP | TNF signaling pathway | 49/2418 | 114/8465 | 6.51e-04 | 3.29e-03 | 2.12e-03 | 49 |
| hsa0466832 | Oral cavity | LP | TNF signaling pathway | 49/2418 | 114/8465 | 6.51e-04 | 3.29e-03 | 2.12e-03 | 49 |
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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 |
| RPS6KA4 | SNV | Missense_Mutation | rs537223935 | c.698C>T | p.Thr233Met | p.T233M | O75676 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-AJ-A3NE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS6KA4 | SNV | Missense_Mutation | c.1735G>A | p.Glu579Lys | p.E579K | O75676 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A0LM-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | cisplatin | SD | |
| RPS6KA4 | SNV | Missense_Mutation | novel | c.599N>T | p.Thr200Ile | p.T200I | O75676 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AP-A1DK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS6KA4 | SNV | Missense_Mutation | novel | c.2030N>A | p.Gly677Asp | p.G677D | O75676 | protein_coding | tolerated(0.23) | benign(0.001) | TCGA-AX-A2HA-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| RPS6KA4 | SNV | Missense_Mutation | rs776640922 | c.913N>A | p.Asp305Asn | p.D305N | O75676 | protein_coding | tolerated(0.57) | benign(0.007) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
| RPS6KA4 | SNV | Missense_Mutation | novel | c.1376N>C | p.Leu459Pro | p.L459P | O75676 | protein_coding | tolerated(0.1) | possibly_damaging(0.811) | TCGA-B5-A1MW-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | PD |
| RPS6KA4 | SNV | Missense_Mutation | novel | c.161N>A | p.Gly54Asp | p.G54D | O75676 | protein_coding | tolerated(0.14) | benign(0.248) | TCGA-B5-A1MX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Hormone Therapy | megace | SD |
| RPS6KA4 | SNV | Missense_Mutation | novel | c.1376N>G | p.Leu459Arg | p.L459R | O75676 | protein_coding | tolerated(0.42) | possibly_damaging(0.616) | TCGA-D1-A0ZO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| RPS6KA4 | SNV | Missense_Mutation | novel | c.278N>A | p.Arg93His | p.R93H | O75676 | protein_coding | deleterious(0.03) | possibly_damaging(0.647) | TCGA-DF-A2KN-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | Unknown | I/II | Unknown | Unknown | SD |
| RPS6KA4 | SNV | Missense_Mutation | c.446T>C | p.Leu149Pro | p.L149P | O75676 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-DI-A0WH-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 |
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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 |
| 8986 | RPS6KA4 | SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, CLINICALLY ACTIONABLE, ENZYME | inhibitor | HESPERADIN | HESPERADIN | 19035792 |
| 8986 | RPS6KA4 | SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, CLINICALLY ACTIONABLE, ENZYME | inhibitor | 252827421 | ||
| 8986 | RPS6KA4 | SERINE THREONINE KINASE, KINASE, DRUGGABLE GENOME, TRANSCRIPTION FACTOR, CLINICALLY ACTIONABLE, ENZYME | LINIFANIB | LINIFANIB |
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