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Gene: RGCC |
Gene summary for RGCC |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | RGCC | Gene ID | 28984 |
| Gene name | regulator of cell cycle | |
| Gene Alias | C13orf15 | |
| Cytomap | 13q14.11 | |
| Gene Type | protein-coding | GO ID | GO:0000079 | UniProtAcc | Q9H4X1 |
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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 |
| 28984 | RGCC | GSM4909282 | Human | Breast | IDC | 5.68e-14 | -4.74e-01 | -0.0288 |
| 28984 | RGCC | GSM4909285 | Human | Breast | IDC | 4.19e-02 | -3.56e-01 | 0.21 |
| 28984 | RGCC | GSM4909286 | Human | Breast | IDC | 5.69e-07 | -4.29e-01 | 0.1081 |
| 28984 | RGCC | GSM4909287 | Human | Breast | IDC | 1.56e-07 | -4.07e-01 | 0.2057 |
| 28984 | RGCC | GSM4909290 | Human | Breast | IDC | 3.39e-10 | -4.79e-01 | 0.2096 |
| 28984 | RGCC | GSM4909291 | Human | Breast | IDC | 3.99e-02 | -3.77e-01 | 0.1753 |
| 28984 | RGCC | GSM4909293 | Human | Breast | IDC | 5.11e-13 | -4.96e-01 | 0.1581 |
| 28984 | RGCC | GSM4909294 | Human | Breast | IDC | 8.83e-15 | -4.95e-01 | 0.2022 |
| 28984 | RGCC | GSM4909296 | Human | Breast | IDC | 8.66e-19 | -5.11e-01 | 0.1524 |
| 28984 | RGCC | GSM4909297 | Human | Breast | IDC | 6.10e-15 | -4.58e-01 | 0.1517 |
| 28984 | RGCC | GSM4909298 | Human | Breast | IDC | 1.61e-06 | -4.26e-01 | 0.1551 |
| 28984 | RGCC | GSM4909301 | Human | Breast | IDC | 3.46e-17 | -5.11e-01 | 0.1577 |
| 28984 | RGCC | GSM4909302 | Human | Breast | IDC | 2.72e-07 | -3.93e-01 | 0.1545 |
| 28984 | RGCC | GSM4909304 | Human | Breast | IDC | 4.99e-18 | -5.09e-01 | 0.1636 |
| 28984 | RGCC | GSM4909306 | Human | Breast | IDC | 3.64e-09 | -4.22e-01 | 0.1564 |
| 28984 | RGCC | GSM4909307 | Human | Breast | IDC | 1.94e-16 | -5.10e-01 | 0.1569 |
| 28984 | RGCC | GSM4909308 | Human | Breast | IDC | 1.15e-13 | -4.86e-01 | 0.158 |
| 28984 | RGCC | GSM4909311 | Human | Breast | IDC | 2.43e-17 | -4.88e-01 | 0.1534 |
| 28984 | RGCC | GSM4909312 | Human | Breast | IDC | 9.92e-21 | -5.23e-01 | 0.1552 |
| 28984 | RGCC | GSM4909313 | Human | Breast | IDC | 1.35e-04 | -3.89e-01 | 0.0391 |
| Page: 1 2 3 4 5 6 7 |
| 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 | ||
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| 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 | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| 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:00362939 | Breast | Precancer | response to decreased oxygen levels | 53/1080 | 322/18723 | 4.09e-12 | 6.84e-10 | 53 |
| GO:00016669 | Breast | Precancer | response to hypoxia | 51/1080 | 307/18723 | 7.33e-12 | 1.11e-09 | 51 |
| GO:00704829 | Breast | Precancer | response to oxygen levels | 55/1080 | 347/18723 | 7.47e-12 | 1.11e-09 | 55 |
| GO:00362948 | Breast | Precancer | cellular response to decreased oxygen levels | 31/1080 | 161/18723 | 2.61e-09 | 2.11e-07 | 31 |
| GO:00714538 | Breast | Precancer | cellular response to oxygen levels | 32/1080 | 177/18723 | 7.32e-09 | 5.52e-07 | 32 |
| GO:00714565 | Breast | Precancer | cellular response to hypoxia | 29/1080 | 151/18723 | 8.98e-09 | 6.50e-07 | 29 |
| GO:00018196 | Breast | Precancer | positive regulation of cytokine production | 52/1080 | 467/18723 | 4.18e-06 | 1.29e-04 | 52 |
| GO:19029059 | Breast | Precancer | positive regulation of supramolecular fiber organization | 28/1080 | 209/18723 | 2.79e-05 | 6.28e-04 | 28 |
| GO:00106319 | Breast | Precancer | epithelial cell migration | 40/1080 | 357/18723 | 4.57e-05 | 9.71e-04 | 40 |
| GO:19029039 | Breast | Precancer | regulation of supramolecular fiber organization | 42/1080 | 383/18723 | 4.92e-05 | 1.04e-03 | 42 |
| GO:00901329 | Breast | Precancer | epithelium migration | 40/1080 | 360/18723 | 5.51e-05 | 1.14e-03 | 40 |
| GO:00506736 | Breast | Precancer | epithelial cell proliferation | 46/1080 | 437/18723 | 6.02e-05 | 1.23e-03 | 46 |
| GO:00435426 | Breast | Precancer | endothelial cell migration | 33/1080 | 279/18723 | 7.28e-05 | 1.44e-03 | 33 |
| GO:00901309 | Breast | Precancer | tissue migration | 40/1080 | 365/18723 | 7.48e-05 | 1.47e-03 | 40 |
| GO:20005738 | Breast | Precancer | positive regulation of DNA biosynthetic process | 13/1080 | 66/18723 | 8.54e-05 | 1.63e-03 | 13 |
| GO:00329709 | Breast | Precancer | regulation of actin filament-based process | 42/1080 | 397/18723 | 1.11e-04 | 2.01e-03 | 42 |
| GO:00514959 | Breast | Precancer | positive regulation of cytoskeleton organization | 28/1080 | 226/18723 | 1.13e-04 | 2.04e-03 | 28 |
| GO:00106329 | Breast | Precancer | regulation of epithelial cell migration | 33/1080 | 292/18723 | 1.74e-04 | 2.86e-03 | 33 |
| GO:00506786 | Breast | Precancer | regulation of epithelial cell proliferation | 40/1080 | 381/18723 | 1.88e-04 | 3.03e-03 | 40 |
| GO:00224079 | Breast | Precancer | regulation of cell-cell adhesion | 45/1080 | 448/18723 | 2.12e-04 | 3.30e-03 | 45 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa0481014 | Breast | IDC | Regulation of actin cytoskeleton | 36/867 | 229/8465 | 5.79e-03 | 3.13e-02 | 2.34e-02 | 36 |
| hsa0481015 | Breast | IDC | Regulation of actin cytoskeleton | 36/867 | 229/8465 | 5.79e-03 | 3.13e-02 | 2.34e-02 | 36 |
| hsa0481023 | Breast | DCIS | Regulation of actin cytoskeleton | 35/846 | 229/8465 | 6.89e-03 | 3.37e-02 | 2.48e-02 | 35 |
| hsa0481033 | Breast | DCIS | Regulation of actin cytoskeleton | 35/846 | 229/8465 | 6.89e-03 | 3.37e-02 | 2.48e-02 | 35 |
| hsa0481016 | Cervix | CC | Regulation of actin cytoskeleton | 64/1267 | 229/8465 | 2.24e-07 | 2.59e-06 | 1.53e-06 | 64 |
| hsa0481017 | Cervix | CC | Regulation of actin cytoskeleton | 64/1267 | 229/8465 | 2.24e-07 | 2.59e-06 | 1.53e-06 | 64 |
| hsa0481028 | Esophagus | ESCC | Regulation of actin cytoskeleton | 133/4205 | 229/8465 | 5.94e-03 | 1.48e-02 | 7.56e-03 | 133 |
| hsa04810112 | Esophagus | ESCC | Regulation of actin cytoskeleton | 133/4205 | 229/8465 | 5.94e-03 | 1.48e-02 | 7.56e-03 | 133 |
| hsa0481026 | Oral cavity | OSCC | Regulation of actin cytoskeleton | 129/3704 | 229/8465 | 7.14e-05 | 2.74e-04 | 1.40e-04 | 129 |
| hsa04810111 | Oral cavity | OSCC | Regulation of actin cytoskeleton | 129/3704 | 229/8465 | 7.14e-05 | 2.74e-04 | 1.40e-04 | 129 |
| hsa0481020 | Prostate | BPH | Regulation of actin cytoskeleton | 80/1718 | 229/8465 | 1.23e-07 | 1.31e-06 | 8.10e-07 | 80 |
| hsa04810110 | Prostate | BPH | Regulation of actin cytoskeleton | 80/1718 | 229/8465 | 1.23e-07 | 1.31e-06 | 8.10e-07 | 80 |
| hsa0481025 | Prostate | Tumor | Regulation of actin cytoskeleton | 84/1791 | 229/8465 | 3.40e-08 | 4.17e-07 | 2.58e-07 | 84 |
| hsa0481035 | Prostate | Tumor | Regulation of actin cytoskeleton | 84/1791 | 229/8465 | 3.40e-08 | 4.17e-07 | 2.58e-07 | 84 |
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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 |
| RGCC | SNV | Missense_Mutation | c.176N>A | p.Arg59His | p.R59H | Q9H4X1 | protein_coding | deleterious(0.03) | probably_damaging(0.917) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| RGCC | SNV | Missense_Mutation | c.194N>A | p.Ser65Asn | p.S65N | Q9H4X1 | protein_coding | tolerated(0.08) | possibly_damaging(0.797) | TCGA-F5-6811-01 | Colorectum | rectum adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| RGCC | SNV | Missense_Mutation | novel | c.206G>A | p.Ser69Asn | p.S69N | Q9H4X1 | protein_coding | tolerated(0.68) | probably_damaging(0.994) | TCGA-EY-A1GO-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Chemotherapy | carboplatin | PD |
| RGCC | SNV | Missense_Mutation | c.382N>T | p.Ala128Ser | p.A128S | Q9H4X1 | protein_coding | deleterious(0) | probably_damaging(0.994) | TCGA-64-5779-01 | Lung | lung adenocarcinoma | Male | <65 | III/IV | Chemotherapy | cisplatin | PD | |
| RGCC | SNV | Missense_Mutation | c.197N>G | p.Ala66Gly | p.A66G | Q9H4X1 | protein_coding | tolerated(0.06) | possibly_damaging(0.721) | TCGA-66-2754-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD |
| Page: 1 |
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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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