|
Gene: SNU13 |
Gene summary for SNU13 |
Gene summary. |
Gene information | Species | Human | Gene symbol | SNU13 | Gene ID | 4809 |
Gene name | small nuclear ribonucleoprotein 13 | |
Gene Alias | 15.5K | |
Cytomap | 22q13.2 | |
Gene Type | protein-coding | GO ID | GO:0000003 | UniProtAcc | P55769 |
Top |
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 |
4809 | SNU13 | GSM4909281 | Human | Breast | IDC | 5.08e-05 | 3.16e-01 | 0.21 |
4809 | SNU13 | GSM4909282 | Human | Breast | IDC | 5.23e-06 | 3.13e-01 | -0.0288 |
4809 | SNU13 | GSM4909288 | Human | Breast | IDC | 2.52e-06 | -1.48e-01 | 0.0988 |
4809 | SNU13 | GSM4909293 | Human | Breast | IDC | 1.94e-11 | -4.02e-01 | 0.1581 |
4809 | SNU13 | GSM4909294 | Human | Breast | IDC | 6.23e-08 | -9.14e-02 | 0.2022 |
4809 | SNU13 | GSM4909296 | Human | Breast | IDC | 1.52e-15 | 5.79e-02 | 0.1524 |
4809 | SNU13 | GSM4909297 | Human | Breast | IDC | 1.48e-34 | -2.18e-01 | 0.1517 |
4809 | SNU13 | GSM4909298 | Human | Breast | IDC | 9.83e-07 | -2.76e-01 | 0.1551 |
4809 | SNU13 | GSM4909302 | Human | Breast | IDC | 1.17e-05 | -3.50e-01 | 0.1545 |
4809 | SNU13 | GSM4909309 | Human | Breast | IDC | 1.62e-08 | -2.40e-01 | 0.0483 |
4809 | SNU13 | GSM4909311 | Human | Breast | IDC | 1.39e-55 | -1.58e-01 | 0.1534 |
4809 | SNU13 | GSM4909312 | Human | Breast | IDC | 1.74e-14 | 1.29e-02 | 0.1552 |
4809 | SNU13 | GSM4909313 | Human | Breast | IDC | 1.07e-06 | -2.56e-01 | 0.0391 |
4809 | SNU13 | GSM4909316 | Human | Breast | IDC | 4.21e-06 | 1.86e-01 | 0.21 |
4809 | SNU13 | GSM4909319 | Human | Breast | IDC | 7.24e-71 | -2.40e-01 | 0.1563 |
4809 | SNU13 | GSM4909320 | Human | Breast | IDC | 1.30e-10 | -3.28e-01 | 0.1575 |
4809 | SNU13 | GSM4909321 | Human | Breast | IDC | 2.16e-24 | -3.45e-01 | 0.1559 |
4809 | SNU13 | brca1 | Human | Breast | Precancer | 1.53e-06 | 3.49e-01 | -0.0338 |
4809 | SNU13 | brca2 | Human | Breast | Precancer | 5.61e-03 | 2.14e-01 | -0.024 |
4809 | SNU13 | M2 | Human | Breast | IDC | 1.94e-03 | -8.08e-02 | 0.21 |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 |
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. |
Top |
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:0000377112 | Skin | cSCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 197/4864 | 320/18723 | 1.45e-41 | 1.14e-38 | 197 |
GO:0000398112 | Skin | cSCC | mRNA splicing, via spliceosome | 197/4864 | 320/18723 | 1.45e-41 | 1.14e-38 | 197 |
GO:001607224 | Skin | cSCC | rRNA metabolic process | 158/4864 | 236/18723 | 4.06e-40 | 2.83e-37 | 158 |
GO:003447017 | Skin | cSCC | ncRNA processing | 215/4864 | 395/18723 | 6.83e-34 | 4.28e-31 | 215 |
GO:007182629 | Skin | cSCC | ribonucleoprotein complex subunit organization | 140/4864 | 227/18723 | 5.54e-30 | 3.16e-27 | 140 |
GO:002261829 | Skin | cSCC | ribonucleoprotein complex assembly | 136/4864 | 220/18723 | 2.60e-29 | 1.25e-26 | 136 |
GO:003466013 | Skin | cSCC | ncRNA metabolic process | 234/4864 | 485/18723 | 1.37e-26 | 4.77e-24 | 234 |
GO:004227429 | Skin | cSCC | ribosomal small subunit biogenesis | 59/4864 | 73/18723 | 1.39e-22 | 2.90e-20 | 59 |
GO:004227328 | Skin | cSCC | ribosomal large subunit biogenesis | 57/4864 | 72/18723 | 4.90e-21 | 8.53e-19 | 57 |
GO:003049012 | Skin | cSCC | maturation of SSU-rRNA | 39/4864 | 50/18723 | 2.04e-14 | 1.40e-12 | 39 |
GO:000047022 | Skin | cSCC | maturation of LSU-rRNA | 22/4864 | 28/18723 | 8.75e-09 | 2.76e-07 | 22 |
GO:00422736 | Stomach | GC | ribosomal large subunit biogenesis | 15/1159 | 72/18723 | 2.81e-05 | 7.88e-04 | 15 |
GO:00422746 | Stomach | GC | ribosomal small subunit biogenesis | 15/1159 | 73/18723 | 3.34e-05 | 9.03e-04 | 15 |
GO:00718266 | Stomach | GC | ribonucleoprotein complex subunit organization | 30/1159 | 227/18723 | 7.06e-05 | 1.57e-03 | 30 |
GO:00226186 | Stomach | GC | ribonucleoprotein complex assembly | 29/1159 | 220/18723 | 9.69e-05 | 1.97e-03 | 29 |
GO:00422546 | Stomach | GC | ribosome biogenesis | 36/1159 | 299/18723 | 1.02e-04 | 2.03e-03 | 36 |
GO:00226136 | Stomach | GC | ribonucleoprotein complex biogenesis | 49/1159 | 463/18723 | 1.72e-04 | 3.02e-03 | 49 |
GO:004227311 | Stomach | CAG with IM | ribosomal large subunit biogenesis | 15/1050 | 72/18723 | 8.76e-06 | 2.99e-04 | 15 |
GO:004227411 | Stomach | CAG with IM | ribosomal small subunit biogenesis | 15/1050 | 73/18723 | 1.05e-05 | 3.51e-04 | 15 |
GO:007182611 | Stomach | CAG with IM | ribonucleoprotein complex subunit organization | 30/1050 | 227/18723 | 1.12e-05 | 3.70e-04 | 30 |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
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 |
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 |
hsa030409 | Endometrium | AEH | Spliceosome | 54/1197 | 217/8465 | 1.47e-05 | 1.65e-04 | 1.21e-04 | 54 |
hsa0304014 | Endometrium | AEH | Spliceosome | 54/1197 | 217/8465 | 1.47e-05 | 1.65e-04 | 1.21e-04 | 54 |
hsa0304024 | Endometrium | EEC | Spliceosome | 54/1237 | 217/8465 | 3.78e-05 | 3.88e-04 | 2.89e-04 | 54 |
hsa0304034 | Endometrium | EEC | Spliceosome | 54/1237 | 217/8465 | 3.78e-05 | 3.88e-04 | 2.89e-04 | 54 |
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 |
Page: 1 2 |
Top |
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 |
Top |
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 |
Top |
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 |
SNU13 | SNV | Missense_Mutation | c.329N>T | p.Ser110Leu | p.S110L | P55769 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-BH-A0HF-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | arimidex | SD | |
SNU13 | SNV | Missense_Mutation | novel | c.152N>G | p.Ser51Cys | p.S51C | P55769 | protein_coding | tolerated(0.18) | benign(0.186) | TCGA-C5-A1M7-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD |
SNU13 | SNV | Missense_Mutation | c.329N>T | p.Ser110Leu | p.S110L | P55769 | protein_coding | deleterious(0.03) | probably_damaging(1) | TCGA-A6-5665-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
SNU13 | SNV | Missense_Mutation | c.52C>A | p.Leu18Ile | p.L18I | P55769 | protein_coding | deleterious(0.02) | benign(0.43) | TCGA-AY-6197-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
SNU13 | SNV | Missense_Mutation | c.301N>A | p.Ala101Thr | p.A101T | P55769 | protein_coding | deleterious(0.04) | benign(0.044) | TCGA-EI-6512-01 | Colorectum | rectum adenocarcinoma | Female | <65 | III/IV | Chemotherapy | folfox | SD | |
SNU13 | SNV | Missense_Mutation | novel | c.76N>A | p.Val26Ile | p.V26I | P55769 | protein_coding | tolerated(0.38) | benign(0.006) | TCGA-A5-A0G1-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SNU13 | SNV | Missense_Mutation | novel | c.123G>T | p.Glu41Asp | p.E41D | P55769 | protein_coding | deleterious(0) | probably_damaging(0.928) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
SNU13 | SNV | Missense_Mutation | novel | c.149T>C | p.Ile50Thr | p.I50T | P55769 | protein_coding | tolerated(0.32) | benign(0.039) | TCGA-AX-A0J0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SNU13 | SNV | Missense_Mutation | novel | c.191N>T | p.Glu64Val | p.E64V | P55769 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-EY-A215-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SNU13 | SNV | Missense_Mutation | novel | c.370G>A | p.Glu124Lys | p.E124K | P55769 | protein_coding | deleterious(0) | benign(0.085) | TCGA-55-8089-01 | Lung | lung adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
Page: 1 2 |
Top |
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 |