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Gene: SNRNP200 |
Gene summary for SNRNP200 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SNRNP200 | Gene ID | 23020 |
| Gene name | small nuclear ribonucleoprotein U5 subunit 200 | |
| Gene Alias | ASCC3L1 | |
| Cytomap | 2q11.2 | |
| Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | O75643 |
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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 |
| 23020 | SNRNP200 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.16e-04 | 3.38e-01 | -0.1808 |
| 23020 | SNRNP200 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.28e-10 | 5.58e-01 | -0.0811 |
| 23020 | SNRNP200 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.57e-04 | 3.69e-01 | -0.1088 |
| 23020 | SNRNP200 | HTA11_347_2000001011 | Human | Colorectum | AD | 2.30e-14 | 5.27e-01 | -0.1954 |
| 23020 | SNRNP200 | HTA11_411_2000001011 | Human | Colorectum | SER | 6.59e-03 | 7.09e-01 | -0.2602 |
| 23020 | SNRNP200 | HTA11_83_2000001011 | Human | Colorectum | SER | 6.66e-04 | 4.23e-01 | -0.1526 |
| 23020 | SNRNP200 | HTA11_696_2000001011 | Human | Colorectum | AD | 4.97e-14 | 4.77e-01 | -0.1464 |
| 23020 | SNRNP200 | HTA11_866_2000001011 | Human | Colorectum | AD | 7.50e-07 | 3.24e-01 | -0.1001 |
| 23020 | SNRNP200 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.04e-10 | 6.25e-01 | -0.059 |
| 23020 | SNRNP200 | HTA11_2992_2000001011 | Human | Colorectum | SER | 1.95e-02 | 4.16e-01 | -0.1706 |
| 23020 | SNRNP200 | HTA11_866_3004761011 | Human | Colorectum | AD | 4.80e-16 | 5.77e-01 | 0.096 |
| 23020 | SNRNP200 | HTA11_7663_2000001011 | Human | Colorectum | SER | 3.97e-03 | 6.42e-01 | 0.0131 |
| 23020 | SNRNP200 | HTA11_10623_2000001011 | Human | Colorectum | AD | 3.16e-08 | 5.15e-01 | -0.0177 |
| 23020 | SNRNP200 | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.05e-02 | 3.80e-01 | 0.0338 |
| 23020 | SNRNP200 | HTA11_7696_3000711011 | Human | Colorectum | AD | 9.78e-11 | 4.72e-01 | 0.0674 |
| 23020 | SNRNP200 | HTA11_6818_2000001011 | Human | Colorectum | AD | 2.37e-02 | 4.04e-01 | 0.0112 |
| 23020 | SNRNP200 | HTA11_7469_2000001011 | Human | Colorectum | AD | 4.13e-03 | 4.61e-01 | -0.0124 |
| 23020 | SNRNP200 | HTA11_6818_2000001021 | Human | Colorectum | AD | 4.60e-06 | 2.55e-01 | 0.0588 |
| 23020 | SNRNP200 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 2.39e-17 | 6.48e-01 | 0.294 |
| 23020 | SNRNP200 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 3.99e-06 | 9.58e-01 | 0.3487 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 | ||
| 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 | ||
| 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:007182618 | Prostate | BPH | ribonucleoprotein complex subunit organization | 87/3107 | 227/18723 | 2.63e-15 | 4.07e-13 | 87 |
| GO:002261818 | Prostate | BPH | ribonucleoprotein complex assembly | 85/3107 | 220/18723 | 3.16e-15 | 4.55e-13 | 85 |
| GO:00016499 | Prostate | BPH | osteoblast differentiation | 75/3107 | 229/18723 | 1.29e-09 | 5.57e-08 | 75 |
| GO:00015039 | Prostate | BPH | ossification | 107/3107 | 408/18723 | 4.31e-07 | 8.83e-06 | 107 |
| GO:00002455 | Prostate | BPH | spliceosomal complex assembly | 24/3107 | 79/18723 | 1.69e-03 | 9.75e-03 | 24 |
| GO:000838019 | Prostate | Tumor | RNA splicing | 153/3246 | 434/18723 | 9.15e-20 | 5.79e-17 | 153 |
| GO:002261319 | Prostate | Tumor | ribonucleoprotein complex biogenesis | 159/3246 | 463/18723 | 3.17e-19 | 1.52e-16 | 159 |
| GO:000037518 | Prostate | Tumor | RNA splicing, via transesterification reactions | 119/3246 | 324/18723 | 3.40e-17 | 1.06e-14 | 119 |
| GO:000037718 | Prostate | Tumor | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 117/3246 | 320/18723 | 9.31e-17 | 2.22e-14 | 117 |
| GO:000039818 | Prostate | Tumor | mRNA splicing, via spliceosome | 117/3246 | 320/18723 | 9.31e-17 | 2.22e-14 | 117 |
| GO:007182619 | Prostate | Tumor | ribonucleoprotein complex subunit organization | 91/3246 | 227/18723 | 3.62e-16 | 7.50e-14 | 91 |
| GO:002261819 | Prostate | Tumor | ribonucleoprotein complex assembly | 89/3246 | 220/18723 | 3.94e-16 | 7.89e-14 | 89 |
| GO:000164915 | Prostate | Tumor | osteoblast differentiation | 77/3246 | 229/18723 | 1.55e-09 | 7.26e-08 | 77 |
| GO:000150314 | Prostate | Tumor | ossification | 109/3246 | 408/18723 | 1.13e-06 | 2.14e-05 | 109 |
| GO:000024512 | Prostate | Tumor | spliceosomal complex assembly | 26/3246 | 79/18723 | 5.68e-04 | 4.11e-03 | 26 |
| GO:000838027 | Skin | AK | RNA splicing | 111/1910 | 434/18723 | 1.85e-20 | 5.49e-17 | 111 |
| GO:002261328 | Skin | AK | ribonucleoprotein complex biogenesis | 108/1910 | 463/18723 | 8.48e-17 | 6.27e-14 | 108 |
| GO:000037526 | Skin | AK | RNA splicing, via transesterification reactions | 85/1910 | 324/18723 | 1.16e-16 | 7.62e-14 | 85 |
| GO:000037726 | Skin | AK | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 84/1910 | 320/18723 | 1.69e-16 | 9.11e-14 | 84 |
| GO:000039826 | Skin | AK | mRNA splicing, via spliceosome | 84/1910 | 320/18723 | 1.69e-16 | 9.11e-14 | 84 |
| Page: 1 2 3 4 5 6 7 8 9 |
| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| hsa03040 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
| hsa030401 | Colorectum | AD | Spliceosome | 73/2092 | 217/8465 | 1.73e-03 | 9.68e-03 | 6.18e-03 | 73 |
| hsa030402 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
| hsa030403 | Colorectum | MSS | Spliceosome | 66/1875 | 217/8465 | 2.58e-03 | 1.27e-02 | 7.81e-03 | 66 |
| hsa030404 | Colorectum | MSI-H | Spliceosome | 37/797 | 217/8465 | 2.49e-04 | 3.23e-03 | 2.70e-03 | 37 |
| hsa030405 | Colorectum | MSI-H | Spliceosome | 37/797 | 217/8465 | 2.49e-04 | 3.23e-03 | 2.70e-03 | 37 |
| hsa0304018 | Esophagus | HGIN | Spliceosome | 79/1383 | 217/8465 | 3.22e-13 | 7.00e-12 | 5.56e-12 | 79 |
| hsa0304019 | Esophagus | HGIN | Spliceosome | 79/1383 | 217/8465 | 3.22e-13 | 7.00e-12 | 5.56e-12 | 79 |
| hsa0304027 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa0304037 | Esophagus | ESCC | Spliceosome | 128/4205 | 217/8465 | 3.31e-03 | 8.79e-03 | 4.50e-03 | 128 |
| hsa030407 | Liver | Cirrhotic | Spliceosome | 102/2530 | 217/8465 | 5.69e-08 | 9.47e-07 | 5.84e-07 | 102 |
| hsa0304012 | Liver | Cirrhotic | Spliceosome | 102/2530 | 217/8465 | 5.69e-08 | 9.47e-07 | 5.84e-07 | 102 |
| hsa0304022 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
| hsa0304032 | Liver | HCC | Spliceosome | 122/4020 | 217/8465 | 5.55e-03 | 1.60e-02 | 8.91e-03 | 122 |
| hsa0304016 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
| hsa0304017 | Oral cavity | OSCC | Spliceosome | 123/3704 | 217/8465 | 7.21e-05 | 2.74e-04 | 1.40e-04 | 123 |
| hsa0304026 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
| hsa0304036 | Oral cavity | LP | Spliceosome | 106/2418 | 217/8465 | 1.30e-10 | 2.40e-09 | 1.55e-09 | 106 |
| hsa0304010 | Prostate | BPH | Spliceosome | 62/1718 | 217/8465 | 1.99e-03 | 7.92e-03 | 4.90e-03 | 62 |
| hsa0304015 | Prostate | BPH | Spliceosome | 62/1718 | 217/8465 | 1.99e-03 | 7.92e-03 | 4.90e-03 | 62 |
| Page: 1 2 |
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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 |
| SNRNP200 | SNV | Missense_Mutation | novel | c.3157N>C | p.Glu1053Gln | p.E1053Q | O75643 | protein_coding | deleterious(0.01) | benign(0.403) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD |
| SNRNP200 | SNV | Missense_Mutation | c.2116N>A | p.Glu706Lys | p.E706K | O75643 | protein_coding | deleterious(0) | benign(0.094) | TCGA-A2-A0CX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | SD | |
| SNRNP200 | SNV | Missense_Mutation | rs867274085 | c.3131N>G | p.Val1044Gly | p.V1044G | O75643 | protein_coding | deleterious(0) | benign(0.378) | TCGA-A7-A26H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | PD |
| SNRNP200 | SNV | Missense_Mutation | novel | c.2000T>G | p.Val667Gly | p.V667G | O75643 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-A8-A06P-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unspecific | SD | |
| SNRNP200 | SNV | Missense_Mutation | novel | c.3613N>C | p.Thr1205Pro | p.T1205P | O75643 | protein_coding | deleterious(0) | benign(0.285) | TCGA-A8-A07W-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | exemestane | SD |
| SNRNP200 | SNV | Missense_Mutation | rs747218822 | c.1864N>A | p.Asp622Asn | p.D622N | O75643 | protein_coding | deleterious(0) | probably_damaging(0.979) | TCGA-AC-A5XS-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | femara | SD |
| SNRNP200 | SNV | Missense_Mutation | c.5377C>G | p.Leu1793Val | p.L1793V | O75643 | protein_coding | tolerated(0.14) | benign(0.175) | TCGA-AN-A041-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| SNRNP200 | SNV | Missense_Mutation | novel | c.879N>T | p.Leu293Phe | p.L293F | O75643 | protein_coding | deleterious(0) | benign(0.234) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SNRNP200 | SNV | Missense_Mutation | c.2692C>T | p.Pro898Ser | p.P898S | O75643 | protein_coding | tolerated(0.06) | benign(0.006) | TCGA-AN-A0XP-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD | |
| SNRNP200 | SNV | Missense_Mutation | c.4201N>G | p.Leu1401Val | p.L1401V | O75643 | protein_coding | tolerated(0.2) | possibly_damaging(0.474) | TCGA-D8-A1XK-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicine+cyclophosphamide | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
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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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