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Gene: RIMS2 |
Gene summary for RIMS2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | RIMS2 | Gene ID | 9699 |
Gene name | regulating synaptic membrane exocytosis 2 | |
Gene Alias | CRSDS | |
Cytomap | 8q22.3 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q9UQ26 |
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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 |
9699 | RIMS2 | CA_HPV_1 | Human | Cervix | CC | 3.40e-02 | -1.29e-01 | 0.0264 |
9699 | RIMS2 | CCI_1 | Human | Cervix | CC | 8.51e-26 | 2.19e+00 | 0.528 |
9699 | RIMS2 | CCI_3 | Human | Cervix | CC | 2.82e-10 | 1.06e+00 | 0.516 |
9699 | RIMS2 | CCII_1 | Human | Cervix | CC | 1.31e-05 | 4.17e-01 | 0.3249 |
9699 | RIMS2 | HTA12-15-2 | Human | Pancreas | PDAC | 1.28e-15 | 1.17e+00 | 0.2315 |
9699 | RIMS2 | HTA12-16-2 | Human | Pancreas | PDAC | 1.71e-02 | 8.77e-01 | 0.0535 |
9699 | RIMS2 | HTA12-23-1 | Human | Pancreas | PDAC | 7.33e-25 | 1.75e+00 | 0.3405 |
9699 | RIMS2 | HTA12-25-1 | Human | Pancreas | PDAC | 1.53e-25 | 1.71e+00 | 0.313 |
9699 | RIMS2 | HTA12-26-1 | Human | Pancreas | PDAC | 3.74e-57 | 2.11e+00 | 0.3728 |
9699 | RIMS2 | HTA12-29-1 | Human | Pancreas | PDAC | 6.88e-123 | 2.08e+00 | 0.3722 |
9699 | RIMS2 | HTA12-30-1 | Human | Pancreas | PDAC | 5.68e-12 | 2.00e+00 | 0.3671 |
9699 | RIMS2 | HTA12-32-1 | Human | Pancreas | PDAC | 1.71e-15 | 1.92e+00 | 0.3624 |
9699 | RIMS2 | HTA12-9-1 | Human | Pancreas | PDAC | 7.97e-06 | 4.76e-01 | 0.1532 |
9699 | RIMS2 | HTA12-9-2 | Human | Pancreas | PDAC | 4.88e-07 | 4.91e-01 | 0.0835 |
9699 | RIMS2 | HTA12-9-3 | Human | Pancreas | PDAC | 3.02e-08 | 8.61e-01 | 0.2045 |
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Transcriptomic changes along malignancy continuum. |
Tissue | Expression Dynamics | Abbreviation |
Cervix | CC: Cervix cancer | |
HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
N_HPV: HPV-infected normal cervix |
∗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:002260410 | Cervix | CC | regulation of cell morphogenesis | 84/2311 | 309/18723 | 1.00e-12 | 4.29e-10 | 84 |
GO:00160498 | Cervix | CC | cell growth | 92/2311 | 482/18723 | 1.16e-05 | 2.49e-04 | 92 |
GO:00459277 | Cervix | CC | positive regulation of growth | 53/2311 | 259/18723 | 1.33e-04 | 1.64e-03 | 53 |
GO:00015588 | Cervix | CC | regulation of cell growth | 77/2311 | 414/18723 | 1.40e-04 | 1.70e-03 | 77 |
GO:00303077 | Cervix | CC | positive regulation of cell growth | 36/2311 | 166/18723 | 4.84e-04 | 4.75e-03 | 36 |
GO:00486386 | Cervix | CC | regulation of developmental growth | 61/2311 | 330/18723 | 7.69e-04 | 6.85e-03 | 61 |
GO:00605606 | Cervix | CC | developmental growth involved in morphogenesis | 46/2311 | 234/18723 | 8.82e-04 | 7.63e-03 | 46 |
GO:00171574 | Cervix | CC | regulation of exocytosis | 39/2311 | 202/18723 | 2.90e-03 | 1.93e-02 | 39 |
GO:19901385 | Cervix | CC | neuron projection extension | 34/2311 | 172/18723 | 3.52e-03 | 2.27e-02 | 34 |
GO:00486395 | Cervix | CC | positive regulation of developmental growth | 33/2311 | 174/18723 | 7.65e-03 | 4.07e-02 | 33 |
GO:00485886 | Cervix | CC | developmental cell growth | 42/2311 | 234/18723 | 7.88e-03 | 4.15e-02 | 42 |
GO:00068873 | Cervix | CC | exocytosis | 59/2311 | 352/18723 | 8.74e-03 | 4.48e-02 | 59 |
GO:00158337 | Cervix | CC | peptide transport | 46/2311 | 264/18723 | 9.69e-03 | 4.78e-02 | 46 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
RIMS2 | SNV | Missense_Mutation | c.236N>T | p.Ser79Leu | p.S79L | Q9UQ26 | protein_coding | deleterious_low_confidence(0) | benign(0.121) | TCGA-56-8626-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
RIMS2 | SNV | Missense_Mutation | c.1247N>T | p.Arg416Leu | p.R416L | Q9UQ26 | protein_coding | tolerated_low_confidence(0.3) | possibly_damaging(0.553) | TCGA-60-2720-01 | Lung | lung squamous cell carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | SD | |
RIMS2 | SNV | Missense_Mutation | c.277N>C | p.Gly93Arg | p.G93R | Q9UQ26 | protein_coding | deleterious_low_confidence(0) | probably_damaging(1) | TCGA-63-A5MS-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
RIMS2 | SNV | Missense_Mutation | c.1613N>C | p.Val538Ala | p.V538A | Q9UQ26 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.798) | TCGA-66-2756-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Unknown | Unknown | SD | |
RIMS2 | SNV | Missense_Mutation | c.521N>C | p.Glu174Ala | p.E174A | Q9UQ26 | protein_coding | tolerated_low_confidence(0.24) | benign(0.003) | TCGA-66-2759-01 | Lung | lung squamous cell carcinoma | Male | >=65 | III/IV | Chemotherapy | carboplatin | CR | |
RIMS2 | SNV | Missense_Mutation | c.3437N>G | p.Ser1146Cys | p.S1146C | Q9UQ26 | protein_coding | deleterious_low_confidence(0) | possibly_damaging(0.847) | TCGA-66-2794-01 | Lung | lung squamous cell carcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
RIMS2 | SNV | Missense_Mutation | novel | c.225N>T | p.Met75Ile | p.M75I | Q9UQ26 | protein_coding | tolerated_low_confidence(1) | benign(0.31) | TCGA-77-6842-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
RIMS2 | SNV | Missense_Mutation | c.757N>G | p.Arg253Gly | p.R253G | Q9UQ26 | protein_coding | tolerated_low_confidence(0.11) | benign(0.001) | TCGA-85-6561-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Chemotherapy | cisplatin | SD | |
RIMS2 | SNV | Missense_Mutation | novel | c.1396N>C | p.Val466Leu | p.V466L | Q9UQ26 | protein_coding | tolerated_low_confidence(0.57) | benign(0.355) | TCGA-85-8355-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
RIMS2 | SNV | Missense_Mutation | novel | c.3419G>C | p.Arg1140Pro | p.R1140P | Q9UQ26 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.997) | TCGA-85-A511-01 | Lung | lung squamous cell carcinoma | Male | <65 | I/II | Unknown | Unknown | PD |
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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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