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Gene: SNRPC |
Gene summary for SNRPC |
Gene summary. |
Gene information | Species | Human | Gene symbol | SNRPC | Gene ID | 6631 |
Gene name | small nuclear ribonucleoprotein polypeptide C | |
Gene Alias | U1C | |
Cytomap | 6p21.31 | |
Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | P09234 |
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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 |
6631 | SNRPC | NCCBC14 | Human | Breast | DCIS | 2.75e-05 | 1.54e-01 | 0.2021 |
6631 | SNRPC | NCCBC5 | Human | Breast | DCIS | 4.67e-11 | 2.70e-01 | 0.2046 |
6631 | SNRPC | P1 | Human | Breast | IDC | 1.28e-11 | -9.54e-02 | 0.1527 |
6631 | SNRPC | P2 | Human | Breast | IDC | 1.07e-08 | 4.90e-01 | 0.21 |
6631 | SNRPC | DCIS2 | Human | Breast | DCIS | 5.04e-53 | 1.57e-01 | 0.0085 |
6631 | SNRPC | HTA11_3410_2000001011 | Human | Colorectum | AD | 2.69e-03 | 1.59e-01 | 0.0155 |
6631 | SNRPC | HTA11_2487_2000001011 | Human | Colorectum | SER | 1.86e-04 | 3.45e-01 | -0.1808 |
6631 | SNRPC | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.05e-09 | 5.08e-01 | -0.0811 |
6631 | SNRPC | HTA11_347_2000001011 | Human | Colorectum | AD | 3.45e-12 | 3.80e-01 | -0.1954 |
6631 | SNRPC | HTA11_696_2000001011 | Human | Colorectum | AD | 1.66e-12 | 4.14e-01 | -0.1464 |
6631 | SNRPC | HTA11_866_2000001011 | Human | Colorectum | AD | 1.14e-04 | 2.09e-01 | -0.1001 |
6631 | SNRPC | HTA11_1391_2000001011 | Human | Colorectum | AD | 4.99e-13 | 5.43e-01 | -0.059 |
6631 | SNRPC | HTA11_546_2000001011 | Human | Colorectum | AD | 7.68e-03 | 3.16e-01 | -0.0842 |
6631 | SNRPC | HTA11_7862_2000001011 | Human | Colorectum | AD | 2.36e-02 | 3.95e-01 | -0.0179 |
6631 | SNRPC | HTA11_866_3004761011 | Human | Colorectum | AD | 4.28e-13 | 4.99e-01 | 0.096 |
6631 | SNRPC | HTA11_10623_2000001011 | Human | Colorectum | AD | 1.18e-04 | 4.75e-01 | -0.0177 |
6631 | SNRPC | HTA11_6801_2000001011 | Human | Colorectum | SER | 3.67e-02 | 3.70e-01 | 0.0171 |
6631 | SNRPC | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.54e-03 | 1.76e-01 | 0.0338 |
6631 | SNRPC | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.99e-13 | 3.69e-01 | 0.0674 |
6631 | SNRPC | HTA11_7469_2000001011 | Human | Colorectum | AD | 5.05e-03 | 4.95e-01 | -0.0124 |
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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:00226139 | Breast | Precancer | ribonucleoprotein complex biogenesis | 79/1080 | 463/18723 | 2.11e-18 | 1.03e-15 | 79 |
GO:00718269 | Breast | Precancer | ribonucleoprotein complex subunit organization | 48/1080 | 227/18723 | 2.68e-15 | 8.45e-13 | 48 |
GO:00226189 | Breast | Precancer | ribonucleoprotein complex assembly | 47/1080 | 220/18723 | 3.47e-15 | 1.03e-12 | 47 |
GO:00083809 | Breast | Precancer | RNA splicing | 65/1080 | 434/18723 | 1.27e-12 | 2.53e-10 | 65 |
GO:00003759 | Breast | Precancer | RNA splicing, via transesterification reactions | 52/1080 | 324/18723 | 1.74e-11 | 2.22e-09 | 52 |
GO:00003779 | Breast | Precancer | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
GO:00003989 | Breast | Precancer | mRNA splicing, via spliceosome | 51/1080 | 320/18723 | 3.55e-11 | 4.04e-09 | 51 |
GO:00003873 | Breast | Precancer | spliceosomal snRNP assembly | 10/1080 | 50/18723 | 4.86e-04 | 6.35e-03 | 10 |
GO:002261314 | Breast | IDC | ribonucleoprotein complex biogenesis | 83/1434 | 463/18723 | 2.01e-13 | 5.20e-11 | 83 |
GO:007182614 | Breast | IDC | ribonucleoprotein complex subunit organization | 52/1434 | 227/18723 | 5.18e-13 | 1.21e-10 | 52 |
GO:002261814 | Breast | IDC | ribonucleoprotein complex assembly | 51/1434 | 220/18723 | 5.32e-13 | 1.21e-10 | 51 |
GO:000838014 | Breast | IDC | RNA splicing | 73/1434 | 434/18723 | 1.27e-10 | 1.57e-08 | 73 |
GO:000037514 | Breast | IDC | RNA splicing, via transesterification reactions | 58/1434 | 324/18723 | 9.44e-10 | 9.58e-08 | 58 |
GO:000037714 | Breast | IDC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
GO:000039814 | Breast | IDC | mRNA splicing, via spliceosome | 57/1434 | 320/18723 | 1.60e-09 | 1.49e-07 | 57 |
GO:000038711 | Breast | IDC | spliceosomal snRNP assembly | 11/1434 | 50/18723 | 1.18e-03 | 1.28e-02 | 11 |
GO:002261324 | Breast | DCIS | ribonucleoprotein complex biogenesis | 83/1390 | 463/18723 | 3.65e-14 | 1.09e-11 | 83 |
GO:007182624 | Breast | DCIS | ribonucleoprotein complex subunit organization | 52/1390 | 227/18723 | 1.54e-13 | 3.95e-11 | 52 |
GO:002261824 | Breast | DCIS | ribonucleoprotein complex assembly | 51/1390 | 220/18723 | 1.60e-13 | 3.95e-11 | 51 |
GO:000838024 | Breast | DCIS | RNA splicing | 73/1390 | 434/18723 | 3.05e-11 | 5.08e-09 | 73 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa030408 | Breast | Precancer | Spliceosome | 39/684 | 217/8465 | 1.44e-06 | 2.27e-05 | 1.74e-05 | 39 |
hsa0304013 | Breast | Precancer | Spliceosome | 39/684 | 217/8465 | 1.44e-06 | 2.27e-05 | 1.74e-05 | 39 |
hsa0304023 | Breast | IDC | Spliceosome | 40/867 | 217/8465 | 1.53e-04 | 1.42e-03 | 1.06e-03 | 40 |
hsa0304033 | Breast | IDC | Spliceosome | 40/867 | 217/8465 | 1.53e-04 | 1.42e-03 | 1.06e-03 | 40 |
hsa0304043 | Breast | DCIS | Spliceosome | 40/846 | 217/8465 | 8.97e-05 | 8.52e-04 | 6.28e-04 | 40 |
hsa0304053 | Breast | DCIS | Spliceosome | 40/846 | 217/8465 | 8.97e-05 | 8.52e-04 | 6.28e-04 | 40 |
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 |
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 |
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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 |
SNRPC | SNV | Missense_Mutation | c.317N>C | p.Met106Thr | p.M106T | P09234 | protein_coding | deleterious(0.01) | benign(0.135) | TCGA-AN-A0FJ-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD | |
SNRPC | SNV | Missense_Mutation | novel | c.152A>G | p.Asp51Gly | p.D51G | P09234 | protein_coding | deleterious(0) | possibly_damaging(0.872) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
SNRPC | SNV | Missense_Mutation | novel | c.72N>A | p.His24Gln | p.H24Q | P09234 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-VS-A8QA-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
SNRPC | SNV | Missense_Mutation | novel | c.155N>C | p.Lys52Thr | p.K52T | P09234 | protein_coding | deleterious(0.04) | benign(0.428) | TCGA-AG-A002-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
SNRPC | SNV | Missense_Mutation | c.113A>G | p.Tyr38Cys | p.Y38C | P09234 | protein_coding | deleterious(0) | possibly_damaging(0.679) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
SNRPC | SNV | Missense_Mutation | novel | c.143N>A | p.Ser48Asn | p.S48N | P09234 | protein_coding | tolerated(0.15) | benign(0.024) | TCGA-AX-A2HD-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
SNRPC | SNV | Missense_Mutation | novel | c.155N>C | p.Lys52Thr | p.K52T | P09234 | protein_coding | deleterious(0.04) | benign(0.428) | TCGA-BK-A6W3-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SNRPC | SNV | Missense_Mutation | novel | c.396N>T | p.Met132Ile | p.M132I | P09234 | protein_coding | deleterious(0.02) | benign(0.38) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SNRPC | SNV | Missense_Mutation | novel | c.359N>A | p.Pro120His | p.P120H | P09234 | protein_coding | deleterious(0) | benign(0.146) | TCGA-EY-A215-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SNRPC | insertion | Frame_Shift_Ins | novel | c.237_238insC | p.Ser82GlnfsTer104 | p.S82Qfs*104 | P09234 | protein_coding | TCGA-B5-A0JU-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | 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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