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Gene: SNRPD2 |
Gene summary for SNRPD2 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | SNRPD2 | Gene ID | 6633 |
| Gene name | small nuclear ribonucleoprotein D2 polypeptide | |
| Gene Alias | SMD2 | |
| Cytomap | 19q13.32 | |
| Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | P62316 |
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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 |
| 6633 | SNRPD2 | CA_HPV_1 | Human | Cervix | CC | 3.53e-05 | -1.89e-01 | 0.0264 |
| 6633 | SNRPD2 | CA_HPV_3 | Human | Cervix | CC | 3.07e-05 | 2.28e-01 | 0.0414 |
| 6633 | SNRPD2 | CCI_1 | Human | Cervix | CC | 2.29e-14 | -8.46e-01 | 0.528 |
| 6633 | SNRPD2 | CCI_2 | Human | Cervix | CC | 2.83e-06 | -6.24e-01 | 0.5249 |
| 6633 | SNRPD2 | CCI_3 | Human | Cervix | CC | 3.80e-13 | -7.51e-01 | 0.516 |
| 6633 | SNRPD2 | CCII_1 | Human | Cervix | CC | 3.01e-27 | -8.53e-01 | 0.3249 |
| 6633 | SNRPD2 | Tumor | Human | Cervix | CC | 3.22e-11 | 3.59e-01 | 0.1241 |
| 6633 | SNRPD2 | sample3 | Human | Cervix | CC | 5.80e-05 | 2.02e-01 | 0.1387 |
| 6633 | SNRPD2 | H2 | Human | Cervix | HSIL_HPV | 4.39e-03 | -3.18e-01 | 0.0632 |
| 6633 | SNRPD2 | L1 | Human | Cervix | CC | 8.04e-05 | -2.22e-01 | 0.0802 |
| 6633 | SNRPD2 | T1 | Human | Cervix | CC | 4.15e-05 | -3.54e-01 | 0.0918 |
| 6633 | SNRPD2 | T3 | Human | Cervix | CC | 8.93e-03 | 2.05e-01 | 0.1389 |
| 6633 | SNRPD2 | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.03e-44 | 9.27e-01 | 0.0155 |
| 6633 | SNRPD2 | HTA11_2487_2000001011 | Human | Colorectum | SER | 5.26e-24 | 9.37e-01 | -0.1808 |
| 6633 | SNRPD2 | HTA11_2951_2000001011 | Human | Colorectum | AD | 2.51e-14 | 8.60e-01 | 0.0216 |
| 6633 | SNRPD2 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.88e-28 | 1.03e+00 | -0.0811 |
| 6633 | SNRPD2 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.30e-08 | 4.10e-01 | -0.1088 |
| 6633 | SNRPD2 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.02e-38 | 8.33e-01 | -0.1954 |
| 6633 | SNRPD2 | HTA11_411_2000001011 | Human | Colorectum | SER | 9.65e-09 | 9.67e-01 | -0.2602 |
| 6633 | SNRPD2 | HTA11_2112_2000001011 | Human | Colorectum | SER | 3.51e-07 | 8.49e-01 | -0.2196 |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Cervix |  | CC: Cervix cancer |
| HSIL_HPV: HPV-infected high-grade squamous intraepithelial lesions | ||
| N_HPV: HPV-infected normal cervix | ||
| Colorectum (GSE201348) |  | FAP: Familial adenomatous polyposis |
| CRC: Colorectal cancer | ||
| Colorectum (HTA11) |  | AD: Adenomas |
| SER: Sessile serrated lesions | ||
| MSI-H: Microsatellite-high colorectal cancer | ||
| MSS: Microsatellite stable colorectal cancer | ||
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid Cancer | ||
| Esophagus |  | ESCC: Esophageal squamous cell carcinoma |
| HGIN: High-grade intraepithelial neoplasias | ||
| LGIN: Low-grade intraepithelial neoplasias | ||
| Liver |  | HCC: Hepatocellular carcinoma |
| NAFLD: Non-alcoholic fatty liver disease | ||
| Oral Cavity |  | EOLP: Erosive Oral lichen planus |
| LP: leukoplakia | ||
| NEOLP: Non-erosive oral lichen planus | ||
| OSCC: Oral squamous cell carcinoma | ||
| Prostate |  | BPH: Benign Prostatic Hyperplasia |
| Skin |  | AK: Actinic keratosis |
| cSCC: Cutaneous squamous cell carcinoma | ||
| SCCIS:squamous cell carcinoma in situ | ||
| Thyroid |  | ATC: Anaplastic thyroid cancer |
| HT: Hashimoto's thyroiditis | ||
| PTC: Papillary thyroid cancer |
| ∗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). |
| 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:002261310 | Cervix | CC | ribonucleoprotein complex biogenesis | 88/2311 | 463/18723 | 2.11e-05 | 3.82e-04 | 88 |
| GO:002261810 | Cervix | CC | ribonucleoprotein complex assembly | 49/2311 | 220/18723 | 2.52e-05 | 4.29e-04 | 49 |
| GO:007182610 | Cervix | CC | ribonucleoprotein complex subunit organization | 49/2311 | 227/18723 | 5.91e-05 | 8.54e-04 | 49 |
| GO:000838010 | Cervix | CC | RNA splicing | 76/2311 | 434/18723 | 9.79e-04 | 8.19e-03 | 76 |
| GO:000037710 | Cervix | CC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
| GO:000039810 | Cervix | CC | mRNA splicing, via spliceosome | 55/2311 | 320/18723 | 6.71e-03 | 3.70e-02 | 55 |
| GO:000037510 | Cervix | CC | RNA splicing, via transesterification reactions | 55/2311 | 324/18723 | 8.61e-03 | 4.44e-02 | 55 |
| GO:002261315 | Cervix | HSIL_HPV | ribonucleoprotein complex biogenesis | 52/737 | 463/18723 | 9.85e-12 | 6.81e-09 | 52 |
| GO:002261815 | Cervix | HSIL_HPV | ribonucleoprotein complex assembly | 29/737 | 220/18723 | 1.19e-08 | 1.30e-06 | 29 |
| GO:007182615 | Cervix | HSIL_HPV | ribonucleoprotein complex subunit organization | 29/737 | 227/18723 | 2.42e-08 | 2.18e-06 | 29 |
| GO:0008380 | Colorectum | AD | RNA splicing | 169/3918 | 434/18723 | 3.59e-18 | 2.04e-15 | 169 |
| GO:0000377 | Colorectum | AD | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000398 | Colorectum | AD | mRNA splicing, via spliceosome | 130/3918 | 320/18723 | 5.88e-16 | 2.16e-13 | 130 |
| GO:0000375 | Colorectum | AD | RNA splicing, via transesterification reactions | 131/3918 | 324/18723 | 7.11e-16 | 2.22e-13 | 131 |
| GO:0022618 | Colorectum | AD | ribonucleoprotein complex assembly | 92/3918 | 220/18723 | 1.49e-12 | 2.60e-10 | 92 |
| GO:0071826 | Colorectum | AD | ribonucleoprotein complex subunit organization | 94/3918 | 227/18723 | 1.70e-12 | 2.87e-10 | 94 |
| GO:0022613 | Colorectum | AD | ribonucleoprotein complex biogenesis | 151/3918 | 463/18723 | 1.96e-09 | 1.39e-07 | 151 |
| GO:0000245 | Colorectum | AD | spliceosomal complex assembly | 33/3918 | 79/18723 | 2.15e-05 | 4.33e-04 | 33 |
| GO:00083801 | Colorectum | SER | RNA splicing | 123/2897 | 434/18723 | 3.84e-12 | 8.41e-10 | 123 |
| GO:00226181 | Colorectum | SER | ribonucleoprotein complex assembly | 69/2897 | 220/18723 | 2.25e-09 | 2.15e-07 | 69 |
| Page: 1 2 3 4 5 6 7 8 9 10 |
| 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 |
| 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 |
| 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 |
| Page: 1 2 |
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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 |
| Page: 1 |
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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. |
| Page: 1 |
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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 |
| SNRPD2 | SNV | Missense_Mutation | c.343N>G | p.Ile115Val | p.I115V | P62316 | protein_coding | tolerated(0.08) | benign(0) | TCGA-D8-A1XQ-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SNRPD2 | SNV | Missense_Mutation | c.314N>T | p.Ser105Leu | p.S105L | P62316 | protein_coding | deleterious(0.04) | benign(0.083) | TCGA-EK-A2IP-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Unknown | Unknown | SD | |
| SNRPD2 | SNV | Missense_Mutation | novel | c.10C>G | p.Leu4Val | p.L4V | P62316 | protein_coding | tolerated(0.15) | benign(0.049) | TCGA-AA-3941-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| SNRPD2 | SNV | Missense_Mutation | c.59N>G | p.Glu20Gly | p.E20G | P62316 | protein_coding | deleterious(0.02) | probably_damaging(0.94) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| SNRPD2 | SNV | Missense_Mutation | novel | c.178N>A | p.Asp60Asn | p.D60N | P62316 | protein_coding | deleterious(0.02) | benign(0.136) | TCGA-AP-A1DV-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SNRPD2 | SNV | Missense_Mutation | novel | c.278A>G | p.Asp93Gly | p.D93G | P62316 | protein_coding | deleterious(0) | benign(0.048) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SNRPD2 | SNV | Missense_Mutation | novel | c.178G>A | p.Asp60Asn | p.D60N | P62316 | protein_coding | deleterious(0.02) | benign(0.136) | TCGA-B5-A3FC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SNRPD2 | SNV | Missense_Mutation | novel | c.252N>T | p.Lys84Asn | p.K84N | P62316 | protein_coding | deleterious(0.03) | possibly_damaging(0.526) | TCGA-FI-A2D0-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| SNRPD2 | SNV | Missense_Mutation | c.226N>A | p.Glu76Lys | p.E76K | P62316 | protein_coding | deleterious(0.04) | benign(0.367) | TCGA-22-5478-01 | Lung | lung squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
| SNRPD2 | SNV | Missense_Mutation | novel | c.41A>C | p.Glu14Ala | p.E14A | P62316 | protein_coding | tolerated(0.17) | benign(0.156) | TCGA-CR-7383-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Chemotherapy | paclitaxel | PR |
| Page: 1 2 |
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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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