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Gene: RBM39 |
Gene summary for RBM39 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RBM39 | Gene ID | 9584 |
| Gene name | RNA binding motif protein 39 | |
| Gene Alias | CAPER | |
| Cytomap | 20q11.22 | |
| Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | Q14498 |
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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 |
| 9584 | RBM39 | GSM4909285 | Human | Breast | IDC | 1.87e-08 | -2.18e-01 | 0.21 |
| 9584 | RBM39 | GSM4909286 | Human | Breast | IDC | 1.93e-13 | -1.30e-01 | 0.1081 |
| 9584 | RBM39 | GSM4909293 | Human | Breast | IDC | 4.71e-03 | 1.91e-01 | 0.1581 |
| 9584 | RBM39 | GSM4909294 | Human | Breast | IDC | 1.19e-05 | -3.18e-01 | 0.2022 |
| 9584 | RBM39 | GSM4909296 | Human | Breast | IDC | 6.36e-11 | -3.30e-01 | 0.1524 |
| 9584 | RBM39 | GSM4909297 | Human | Breast | IDC | 2.36e-20 | -1.73e-01 | 0.1517 |
| 9584 | RBM39 | GSM4909301 | Human | Breast | IDC | 9.10e-14 | 3.60e-01 | 0.1577 |
| 9584 | RBM39 | GSM4909304 | Human | Breast | IDC | 3.12e-04 | -2.22e-01 | 0.1636 |
| 9584 | RBM39 | GSM4909308 | Human | Breast | IDC | 8.20e-04 | 1.12e-02 | 0.158 |
| 9584 | RBM39 | GSM4909311 | Human | Breast | IDC | 3.07e-49 | -5.54e-01 | 0.1534 |
| 9584 | RBM39 | GSM4909312 | Human | Breast | IDC | 2.64e-08 | -8.41e-02 | 0.1552 |
| 9584 | RBM39 | GSM4909313 | Human | Breast | IDC | 1.77e-03 | -2.19e-01 | 0.0391 |
| 9584 | RBM39 | GSM4909315 | Human | Breast | IDC | 1.49e-08 | -3.94e-01 | 0.21 |
| 9584 | RBM39 | GSM4909316 | Human | Breast | IDC | 1.20e-07 | -6.11e-01 | 0.21 |
| 9584 | RBM39 | GSM4909319 | Human | Breast | IDC | 7.58e-58 | -5.08e-01 | 0.1563 |
| 9584 | RBM39 | GSM4909320 | Human | Breast | IDC | 2.52e-08 | 1.12e-01 | 0.1575 |
| 9584 | RBM39 | GSM4909321 | Human | Breast | IDC | 2.07e-11 | 5.79e-02 | 0.1559 |
| 9584 | RBM39 | brca1 | Human | Breast | Precancer | 4.17e-02 | -1.45e-01 | -0.0338 |
| 9584 | RBM39 | brca2 | Human | Breast | Precancer | 4.27e-09 | -1.45e-02 | -0.024 |
| 9584 | RBM39 | brca3 | Human | Breast | Precancer | 4.47e-04 | 2.06e-02 | -0.0263 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Breast |  | IDC: Invasive ductal carcinoma |
| DCIS: Ductal carcinoma in situ | ||
| Precancer(BRCA1-mut): Precancerous lesion from BRCA1 mutation carriers | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Lung |  | AAH: Atypical adenomatous hyperplasia |
| AIS: Adenocarcinoma in situ | ||
| IAC: Invasive lung adenocarcinoma | ||
| MIA: Minimally invasive adenocarcinoma | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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:00083809 | Breast | Precancer | RNA splicing | 65/1080 | 434/18723 | 1.27e-12 | 2.53e-10 | 65 |
| GO:00434849 | Breast | Precancer | regulation of RNA splicing | 34/1080 | 148/18723 | 2.66e-12 | 4.75e-10 | 34 |
| GO:00003759 | Breast | Precancer | RNA splicing, via transesterification reactions | 52/1080 | 324/18723 | 1.74e-11 | 2.22e-09 | 52 |
| GO:00003779 | Breast | Precancer | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:00003989 | Breast | Precancer | mRNA splicing, via spliceosome | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
| GO:00480249 | Breast | Precancer | regulation of mRNA splicing, via spliceosome | 22/1080 | 101/18723 | 5.29e-08 | 3.18e-06 | 22 |
| GO:19033118 | Breast | Precancer | regulation of mRNA metabolic process | 38/1080 | 288/18723 | 1.63e-06 | 5.97e-05 | 38 |
| GO:00506848 | Breast | Precancer | regulation of mRNA processing | 23/1080 | 137/18723 | 3.49e-06 | 1.13e-04 | 23 |
| GO:000838014 | Breast | IDC | RNA splicing | 73/1434 | 434/18723 | 1.27e-10 | 1.57e-08 | 73 |
| GO:004348414 | Breast | IDC | regulation of RNA splicing | 36/1434 | 148/18723 | 3.32e-10 | 3.77e-08 | 36 |
| GO:000037514 | Breast | IDC | RNA splicing, via transesterification reactions | 58/1434 | 324/18723 | 9.44e-10 | 9.58e-08 | 58 |
| GO:000037714 | Breast | IDC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
| GO:000039814 | Breast | IDC | mRNA splicing, via spliceosome | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
| GO:004802414 | Breast | IDC | regulation of mRNA splicing, via spliceosome | 23/1434 | 101/18723 | 1.74e-06 | 7.28e-05 | 23 |
| GO:005068413 | Breast | IDC | regulation of mRNA processing | 24/1434 | 137/18723 | 1.09e-04 | 2.04e-03 | 24 |
| GO:190331113 | Breast | IDC | regulation of mRNA metabolic process | 40/1434 | 288/18723 | 1.79e-04 | 3.01e-03 | 40 |
| GO:000838024 | Breast | DCIS | RNA splicing | 73/1390 | 434/18723 | 3.05e-11 | 5.08e-09 | 73 |
| GO:004348424 | Breast | DCIS | regulation of RNA splicing | 36/1390 | 148/18723 | 1.40e-10 | 1.69e-08 | 36 |
| GO:000037524 | Breast | DCIS | RNA splicing, via transesterification reactions | 58/1390 | 324/18723 | 2.89e-10 | 3.34e-08 | 58 |
| GO:000037724 | Breast | DCIS | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 57/1390 | 320/18723 | 5.01e-10 | 5.35e-08 | 57 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| RBM39 | SNV | Missense_Mutation | novel | c.995C>A | p.Ala332Asp | p.A332D | Q14498 | protein_coding | tolerated(0.15) | benign(0.147) | TCGA-A2-A0EN-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | tamoxiphen | SD |
| RBM39 | SNV | Missense_Mutation | novel | c.1406C>T | p.Ser469Leu | p.S469L | Q14498 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-BH-A2L8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | cytoxan | CR |
| RBM39 | SNV | Missense_Mutation | c.1386T>A | p.His462Gln | p.H462Q | Q14498 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D8-A1JB-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| RBM39 | SNV | Missense_Mutation | c.452N>T | p.Asp151Val | p.D151V | Q14498 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-D8-A1JH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | nolvadex | SD | |
| RBM39 | SNV | Missense_Mutation | c.1303N>G | p.Gln435Glu | p.Q435E | Q14498 | protein_coding | tolerated(0.34) | benign(0.024) | TCGA-DS-A0VM-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | PD | |
| RBM39 | SNV | Missense_Mutation | c.846N>A | p.Met282Ile | p.M282I | Q14498 | protein_coding | tolerated(0.41) | benign(0.055) | TCGA-EK-A2PM-01 | Cervix | cervical & endocervical cancer | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RBM39 | SNV | Missense_Mutation | c.326N>A | p.Arg109Gln | p.R109Q | Q14498 | protein_coding | tolerated(0.2) | possibly_damaging(0.885) | TCGA-VS-A9UM-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| RBM39 | SNV | Missense_Mutation | c.326N>A | p.Arg109Gln | p.R109Q | Q14498 | protein_coding | tolerated(0.2) | possibly_damaging(0.885) | TCGA-A6-5661-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RBM39 | SNV | Missense_Mutation | c.1048N>T | p.Asp350Tyr | p.D350Y | Q14498 | protein_coding | deleterious(0) | probably_damaging(0.971) | TCGA-AA-3510-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| RBM39 | SNV | Missense_Mutation | novel | c.1006N>G | p.Ser336Gly | p.S336G | Q14498 | protein_coding | tolerated(0.43) | benign(0.07) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD |
| Page: 1 2 3 4 5 6 7 |
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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 |
| Page: 1 |
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