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Gene: SNRPD3 |
Gene summary for SNRPD3 |
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Gene information | Species | Human | Gene symbol | SNRPD3 | Gene ID | 6634 |
Gene name | small nuclear ribonucleoprotein D3 polypeptide | |
Gene Alias | SMD3 | |
Cytomap | 22q11.23 | |
Gene Type | protein-coding | GO ID | GO:0000375 | UniProtAcc | P62318 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
6634 | SNRPD3 | GSM4909280 | Human | Breast | Precancer | 1.91e-04 | -3.84e-01 | 0.0305 |
6634 | SNRPD3 | GSM4909281 | Human | Breast | IDC | 1.94e-14 | 5.27e-01 | 0.21 |
6634 | SNRPD3 | GSM4909282 | Human | Breast | IDC | 2.43e-25 | 6.24e-01 | -0.0288 |
6634 | SNRPD3 | GSM4909285 | Human | Breast | IDC | 1.64e-29 | 6.85e-01 | 0.21 |
6634 | SNRPD3 | GSM4909287 | Human | Breast | IDC | 4.37e-14 | 5.13e-01 | 0.2057 |
6634 | SNRPD3 | GSM4909288 | Human | Breast | IDC | 6.79e-06 | 3.21e-01 | 0.0988 |
6634 | SNRPD3 | GSM4909290 | Human | Breast | IDC | 1.33e-02 | 3.25e-01 | 0.2096 |
6634 | SNRPD3 | GSM4909293 | Human | Breast | IDC | 1.49e-02 | 2.14e-01 | 0.1581 |
6634 | SNRPD3 | GSM4909294 | Human | Breast | IDC | 2.86e-24 | 5.93e-01 | 0.2022 |
6634 | SNRPD3 | GSM4909296 | Human | Breast | IDC | 5.27e-15 | 2.74e-01 | 0.1524 |
6634 | SNRPD3 | GSM4909297 | Human | Breast | IDC | 2.15e-14 | -4.77e-02 | 0.1517 |
6634 | SNRPD3 | GSM4909298 | Human | Breast | IDC | 1.69e-03 | 3.03e-01 | 0.1551 |
6634 | SNRPD3 | GSM4909304 | Human | Breast | IDC | 4.34e-11 | 3.80e-01 | 0.1636 |
6634 | SNRPD3 | GSM4909311 | Human | Breast | IDC | 8.41e-32 | -1.19e-01 | 0.1534 |
6634 | SNRPD3 | GSM4909312 | Human | Breast | IDC | 2.32e-09 | 1.53e-02 | 0.1552 |
6634 | SNRPD3 | GSM4909313 | Human | Breast | IDC | 1.73e-02 | -1.63e-01 | 0.0391 |
6634 | SNRPD3 | GSM4909315 | Human | Breast | IDC | 4.06e-06 | 3.66e-01 | 0.21 |
6634 | SNRPD3 | GSM4909316 | Human | Breast | IDC | 4.86e-06 | 4.11e-01 | 0.21 |
6634 | SNRPD3 | GSM4909317 | Human | Breast | IDC | 7.87e-12 | 4.79e-01 | 0.1355 |
6634 | SNRPD3 | GSM4909318 | Human | Breast | IDC | 6.08e-23 | 8.47e-01 | 0.2031 |
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∗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 |
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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 |
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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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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 |
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 |
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Cell-cell communication analysis |
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Ligand | Receptor | LRpair | Pathway | Tissue | Disease Stage |
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Single-cell gene regulatory network inference analysis |
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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 |
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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 |
SNRPD3 | SNV | Missense_Mutation | c.190N>A | p.Arg64Ser | p.R64S | P62318 | protein_coding | deleterious(0) | probably_damaging(0.966) | TCGA-HC-7075-01 | Prostate | prostate adenocarcinoma | Male | <65 | 6 | Unknown | Unknown | SD | |
SNRPD3 | SNV | Missense_Mutation | c.182N>C | p.Val61Ala | p.V61A | P62318 | protein_coding | deleterious(0.02) | possibly_damaging(0.461) | TCGA-CG-5723-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SNRPD3 | SNV | Missense_Mutation | rs775024855 | c.13N>A | p.Val5Met | p.V5M | P62318 | protein_coding | deleterious(0) | benign(0.206) | TCGA-HU-8602-01 | Stomach | stomach adenocarcinoma | Female | <65 | I/II | Chemotherapy | xeloda | CR |
SNRPD3 | SNV | Missense_Mutation | novel | c.352N>T | p.Arg118Cys | p.R118C | P62318 | protein_coding | tolerated(0.11) | benign(0.155) | TCGA-VQ-A91D-01 | Stomach | stomach adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | fluorouracil | PD |
SNRPD3 | deletion | Frame_Shift_Del | novel | c.70delA | p.Thr24ProfsTer16 | p.T24Pfs*16 | P62318 | protein_coding | TCGA-BR-6452-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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Related drugs of malignant transformation related genes |
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(DGIdb 4.0) |
Entrez ID | Symbol | Category | Interaction Types | Drug Claim Name | Drug Name | PMIDs |
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