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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 |
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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:190290518 | Prostate | BPH | positive regulation of supramolecular fiber organization | 84/3107 | 209/18723 | 3.00e-16 | 5.63e-14 | 84 |
GO:003295618 | Prostate | BPH | regulation of actin cytoskeleton organization | 118/3107 | 358/18723 | 1.51e-14 | 1.87e-12 | 118 |
GO:005101718 | Prostate | BPH | actin filament bundle assembly | 65/3107 | 157/18723 | 1.31e-13 | 1.38e-11 | 65 |
GO:005149516 | Prostate | BPH | positive regulation of cytoskeleton organization | 83/3107 | 226/18723 | 1.83e-13 | 1.86e-11 | 83 |
GO:011005318 | Prostate | BPH | regulation of actin filament organization | 96/3107 | 278/18723 | 1.90e-13 | 1.89e-11 | 96 |
GO:006157218 | Prostate | BPH | actin filament bundle organization | 65/3107 | 161/18723 | 5.29e-13 | 4.75e-11 | 65 |
GO:007048217 | Prostate | BPH | response to oxygen levels | 104/3107 | 347/18723 | 3.13e-10 | 1.67e-08 | 104 |
GO:003629317 | Prostate | BPH | response to decreased oxygen levels | 96/3107 | 322/18723 | 2.03e-09 | 8.26e-08 | 96 |
GO:009013216 | Prostate | BPH | epithelium migration | 104/3107 | 360/18723 | 2.96e-09 | 1.15e-07 | 104 |
GO:009013016 | Prostate | BPH | tissue migration | 105/3107 | 365/18723 | 3.21e-09 | 1.24e-07 | 105 |
GO:000166617 | Prostate | BPH | response to hypoxia | 92/3107 | 307/18723 | 3.29e-09 | 1.27e-07 | 92 |
GO:001063116 | Prostate | BPH | epithelial cell migration | 103/3107 | 357/18723 | 3.80e-09 | 1.44e-07 | 103 |
GO:000166717 | Prostate | BPH | ameboidal-type cell migration | 128/3107 | 475/18723 | 5.69e-09 | 2.05e-07 | 128 |
GO:001063216 | Prostate | BPH | regulation of epithelial cell migration | 87/3107 | 292/18723 | 1.18e-08 | 3.87e-07 | 87 |
GO:003003817 | Prostate | BPH | contractile actin filament bundle assembly | 42/3107 | 106/18723 | 1.27e-08 | 4.07e-07 | 42 |
GO:004314917 | Prostate | BPH | stress fiber assembly | 42/3107 | 106/18723 | 1.27e-08 | 4.07e-07 | 42 |
GO:003223117 | Prostate | BPH | regulation of actin filament bundle assembly | 41/3107 | 105/18723 | 3.08e-08 | 8.91e-07 | 41 |
GO:003103215 | Prostate | BPH | actomyosin structure organization | 63/3107 | 196/18723 | 5.78e-08 | 1.57e-06 | 63 |
GO:011002018 | Prostate | BPH | regulation of actomyosin structure organization | 39/3107 | 100/18723 | 6.90e-08 | 1.82e-06 | 39 |
GO:00506739 | Prostate | BPH | epithelial cell proliferation | 116/3107 | 437/18723 | 7.12e-08 | 1.85e-06 | 116 |
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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 |
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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 |
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 |
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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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