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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 |
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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:00003772 | Colorectum | MSS | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 121/3467 | 320/18723 | 2.52e-16 | 8.27e-14 | 121 |
GO:00003982 | Colorectum | MSS | mRNA splicing, via spliceosome | 121/3467 | 320/18723 | 2.52e-16 | 8.27e-14 | 121 |
GO:00003752 | Colorectum | MSS | RNA splicing, via transesterification reactions | 122/3467 | 324/18723 | 2.75e-16 | 8.58e-14 | 122 |
GO:00718262 | Colorectum | MSS | ribonucleoprotein complex subunit organization | 90/3467 | 227/18723 | 6.88e-14 | 1.78e-11 | 90 |
GO:00226182 | Colorectum | MSS | ribonucleoprotein complex assembly | 88/3467 | 220/18723 | 7.12e-14 | 1.78e-11 | 88 |
GO:00226132 | Colorectum | MSS | ribonucleoprotein complex biogenesis | 144/3467 | 463/18723 | 2.76e-11 | 3.67e-09 | 144 |
GO:00002451 | Colorectum | MSS | spliceosomal complex assembly | 31/3467 | 79/18723 | 1.33e-05 | 3.07e-04 | 31 |
GO:00016492 | Colorectum | MSS | osteoblast differentiation | 64/3467 | 229/18723 | 2.91e-04 | 3.83e-03 | 64 |
GO:00015032 | Colorectum | MSS | ossification | 96/3467 | 408/18723 | 6.09e-03 | 4.07e-02 | 96 |
GO:00226183 | Colorectum | MSI-H | ribonucleoprotein complex assembly | 62/1319 | 220/18723 | 7.13e-22 | 8.32e-19 | 62 |
GO:00718263 | Colorectum | MSI-H | ribonucleoprotein complex subunit organization | 63/1319 | 227/18723 | 8.08e-22 | 8.32e-19 | 63 |
GO:00226133 | Colorectum | MSI-H | ribonucleoprotein complex biogenesis | 95/1319 | 463/18723 | 1.04e-21 | 8.32e-19 | 95 |
GO:00083803 | Colorectum | MSI-H | RNA splicing | 82/1319 | 434/18723 | 1.22e-16 | 4.53e-14 | 82 |
GO:00003753 | Colorectum | MSI-H | RNA splicing, via transesterification reactions | 67/1319 | 324/18723 | 7.99e-16 | 2.61e-13 | 67 |
GO:00003773 | Colorectum | MSI-H | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 66/1319 | 320/18723 | 1.51e-15 | 4.41e-13 | 66 |
GO:00003983 | Colorectum | MSI-H | mRNA splicing, via spliceosome | 66/1319 | 320/18723 | 1.51e-15 | 4.41e-13 | 66 |
GO:00002452 | Colorectum | MSI-H | spliceosomal complex assembly | 14/1319 | 79/18723 | 1.14e-03 | 1.90e-02 | 14 |
GO:00083804 | Colorectum | FAP | RNA splicing | 108/2622 | 434/18723 | 7.90e-10 | 1.86e-07 | 108 |
GO:00003754 | Colorectum | FAP | RNA splicing, via transesterification reactions | 84/2622 | 324/18723 | 8.06e-09 | 1.10e-06 | 84 |
GO:00003774 | Colorectum | FAP | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 83/2622 | 320/18723 | 9.66e-09 | 1.23e-06 | 83 |
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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 |
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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 |
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 |
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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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