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Gene: SNRPD1 |
Gene summary for SNRPD1 |
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Gene information | Species | Human | Gene symbol | SNRPD1 | Gene ID | 6632 |
Gene name | small nuclear ribonucleoprotein D1 polypeptide | |
Gene Alias | HsT2456 | |
Cytomap | 18q11.2 | |
Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | P62314 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
6632 | SNRPD1 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.35e-09 | 3.86e-01 | 0.3859 |
6632 | SNRPD1 | AEH-subject1 | Human | Endometrium | AEH | 1.98e-13 | -3.45e-01 | -0.3059 |
6632 | SNRPD1 | AEH-subject2 | Human | Endometrium | AEH | 7.79e-16 | -4.33e-01 | -0.2525 |
6632 | SNRPD1 | AEH-subject3 | Human | Endometrium | AEH | 7.64e-17 | -3.24e-01 | -0.2576 |
6632 | SNRPD1 | AEH-subject4 | Human | Endometrium | AEH | 1.19e-12 | -4.70e-01 | -0.2657 |
6632 | SNRPD1 | AEH-subject5 | Human | Endometrium | AEH | 8.31e-14 | -3.66e-01 | -0.2953 |
6632 | SNRPD1 | EEC-subject1 | Human | Endometrium | EEC | 1.03e-16 | -3.94e-01 | -0.2682 |
6632 | SNRPD1 | EEC-subject2 | Human | Endometrium | EEC | 5.55e-20 | -4.64e-01 | -0.2607 |
6632 | SNRPD1 | EEC-subject3 | Human | Endometrium | EEC | 3.69e-44 | -4.73e-01 | -0.2525 |
6632 | SNRPD1 | EEC-subject4 | Human | Endometrium | EEC | 1.52e-12 | -3.75e-01 | -0.2571 |
6632 | SNRPD1 | EEC-subject5 | Human | Endometrium | EEC | 2.43e-11 | -3.20e-01 | -0.249 |
6632 | SNRPD1 | GSM5276934 | Human | Endometrium | EEC | 1.51e-04 | 4.80e-02 | -0.0913 |
6632 | SNRPD1 | GSM5276937 | Human | Endometrium | EEC | 6.61e-07 | 2.64e-01 | -0.0897 |
6632 | SNRPD1 | GSM6177620_NYU_UCEC1_lib1_lib1 | Human | Endometrium | EEC | 9.32e-30 | -3.98e-01 | -0.1869 |
6632 | SNRPD1 | GSM6177620_NYU_UCEC1_lib2_lib2 | Human | Endometrium | EEC | 1.04e-27 | -2.03e-01 | -0.1875 |
6632 | SNRPD1 | GSM6177620_NYU_UCEC1_lib3_lib3 | Human | Endometrium | EEC | 7.43e-32 | -2.73e-01 | -0.1883 |
6632 | SNRPD1 | GSM6177621_NYU_UCEC2_lib1_lib1 | Human | Endometrium | EEC | 1.74e-37 | -3.34e-01 | -0.1934 |
6632 | SNRPD1 | GSM6177622_NYU_UCEC3_lib1_lib1 | Human | Endometrium | EEC | 9.50e-53 | -3.24e-01 | -0.1917 |
6632 | SNRPD1 | GSM6177622_NYU_UCEC3_lib2_lib2 | Human | Endometrium | EEC | 3.79e-52 | -3.99e-01 | -0.1916 |
6632 | SNRPD1 | GSM6177623_NYU_UCEC3_Vis | Human | Endometrium | EEC | 1.58e-06 | -1.50e-01 | -0.1269 |
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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). |
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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 |
SNRPD1 | SNV | Missense_Mutation | c.182N>A | p.Arg61Gln | p.R61Q | P62314 | protein_coding | deleterious(0) | probably_damaging(0.988) | TCGA-AP-A056-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
SNRPD1 | SNV | Missense_Mutation | rs572142783 | c.196N>T | p.Arg66Trp | p.R66W | P62314 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
SNRPD1 | SNV | Missense_Mutation | novel | c.154N>T | p.Pro52Ser | p.P52S | P62314 | protein_coding | deleterious(0.03) | benign(0.3) | TCGA-AX-A1CE-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unspecific | Paclitaxel | SD |
SNRPD1 | SNV | Missense_Mutation | novel | c.39A>T | p.Glu13Asp | p.E13D | P62314 | protein_coding | deleterious(0) | probably_damaging(0.953) | TCGA-B5-A1MR-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
SNRPD1 | SNV | Missense_Mutation | novel | c.155N>A | p.Pro52His | p.P52H | P62314 | protein_coding | deleterious(0.04) | probably_damaging(0.957) | TCGA-B5-A1MX-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Hormone Therapy | megace | SD |
SNRPD1 | SNV | Missense_Mutation | novel | c.184N>A | p.Gly62Arg | p.G62R | P62314 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-EO-A22U-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
SNRPD1 | SNV | Missense_Mutation | c.322N>T | p.Arg108Cys | p.R108C | P62314 | protein_coding | tolerated(0.06) | probably_damaging(0.973) | TCGA-78-7156-01 | Lung | lung adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD | |
SNRPD1 | SNV | Missense_Mutation | c.226N>G | p.Leu76Val | p.L76V | P62314 | protein_coding | deleterious(0.01) | possibly_damaging(0.78) | TCGA-56-5897-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
SNRPD1 | SNV | Missense_Mutation | c.328N>T | p.Arg110Cys | p.R110C | P62314 | protein_coding | deleterious(0) | probably_damaging(0.973) | TCGA-CG-4305-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Chemotherapy | cisplatin | CR |
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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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