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Gene: GEMIN2 |
Gene summary for GEMIN2 |
Gene summary. |
Gene information | Species | Human | Gene symbol | GEMIN2 | Gene ID | 8487 |
Gene name | gem nuclear organelle associated protein 2 | |
Gene Alias | SIP1 | |
Cytomap | 14q21.1 | |
Gene Type | protein-coding | GO ID | GO:0000245 | UniProtAcc | O14893 |
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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 |
8487 | GEMIN2 | P54T-E | Human | Esophagus | ESCC | 5.82e-06 | 1.44e-01 | 0.0975 |
8487 | GEMIN2 | P57T-E | Human | Esophagus | ESCC | 3.45e-07 | 1.66e-01 | 0.0926 |
8487 | GEMIN2 | P61T-E | Human | Esophagus | ESCC | 2.66e-21 | 4.11e-01 | 0.099 |
8487 | GEMIN2 | P62T-E | Human | Esophagus | ESCC | 1.79e-16 | 2.52e-01 | 0.1302 |
8487 | GEMIN2 | P65T-E | Human | Esophagus | ESCC | 2.63e-13 | 2.46e-01 | 0.0978 |
8487 | GEMIN2 | P74T-E | Human | Esophagus | ESCC | 2.44e-20 | 4.57e-01 | 0.1479 |
8487 | GEMIN2 | P75T-E | Human | Esophagus | ESCC | 1.29e-27 | 5.27e-01 | 0.1125 |
8487 | GEMIN2 | P76T-E | Human | Esophagus | ESCC | 8.09e-06 | 1.18e-01 | 0.1207 |
8487 | GEMIN2 | P79T-E | Human | Esophagus | ESCC | 1.93e-14 | 3.21e-01 | 0.1154 |
8487 | GEMIN2 | P80T-E | Human | Esophagus | ESCC | 3.61e-13 | 3.24e-01 | 0.155 |
8487 | GEMIN2 | P82T-E | Human | Esophagus | ESCC | 6.28e-04 | 1.79e-01 | 0.1072 |
8487 | GEMIN2 | P83T-E | Human | Esophagus | ESCC | 1.14e-30 | 6.74e-01 | 0.1738 |
8487 | GEMIN2 | P84T-E | Human | Esophagus | ESCC | 1.67e-05 | 3.26e-01 | 0.0933 |
8487 | GEMIN2 | P89T-E | Human | Esophagus | ESCC | 6.10e-11 | 5.58e-01 | 0.1752 |
8487 | GEMIN2 | P91T-E | Human | Esophagus | ESCC | 6.28e-18 | 1.37e+00 | 0.1828 |
8487 | GEMIN2 | P107T-E | Human | Esophagus | ESCC | 2.91e-17 | 3.21e-01 | 0.171 |
8487 | GEMIN2 | P127T-E | Human | Esophagus | ESCC | 1.65e-03 | 7.11e-02 | 0.0826 |
8487 | GEMIN2 | P128T-E | Human | Esophagus | ESCC | 1.32e-46 | 1.05e+00 | 0.1241 |
8487 | GEMIN2 | P130T-E | Human | Esophagus | ESCC | 3.29e-30 | 6.30e-01 | 0.1676 |
8487 | GEMIN2 | C04 | Human | Oral cavity | OSCC | 5.74e-13 | 6.40e-01 | 0.2633 |
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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:0022613111 | Esophagus | ESCC | ribonucleoprotein complex biogenesis | 365/8552 | 463/18723 | 1.74e-49 | 1.11e-45 | 365 |
GO:0008380111 | Esophagus | ESCC | RNA splicing | 336/8552 | 434/18723 | 1.74e-42 | 3.67e-39 | 336 |
GO:0000375111 | Esophagus | ESCC | RNA splicing, via transesterification reactions | 248/8552 | 324/18723 | 3.05e-30 | 1.49e-27 | 248 |
GO:0000377111 | Esophagus | ESCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
GO:0000398111 | Esophagus | ESCC | mRNA splicing, via spliceosome | 244/8552 | 320/18723 | 2.52e-29 | 1.07e-26 | 244 |
GO:0051098111 | Esophagus | ESCC | regulation of binding | 251/8552 | 363/18723 | 6.73e-20 | 8.46e-18 | 251 |
GO:0071826111 | Esophagus | ESCC | ribonucleoprotein complex subunit organization | 166/8552 | 227/18723 | 2.94e-17 | 2.42e-15 | 166 |
GO:0022618111 | Esophagus | ESCC | ribonucleoprotein complex assembly | 159/8552 | 220/18723 | 8.19e-16 | 5.71e-14 | 159 |
GO:0051100111 | Esophagus | ESCC | negative regulation of binding | 109/8552 | 162/18723 | 2.10e-08 | 4.03e-07 | 109 |
GO:19052142 | Esophagus | ESCC | regulation of RNA binding | 12/8552 | 12/18723 | 8.21e-05 | 6.01e-04 | 12 |
GO:000024514 | Esophagus | ESCC | spliceosomal complex assembly | 48/8552 | 79/18723 | 4.93e-03 | 1.89e-02 | 48 |
GO:00003875 | Esophagus | ESCC | spliceosomal snRNP assembly | 32/8552 | 50/18723 | 6.90e-03 | 2.52e-02 | 32 |
GO:002261320 | Oral cavity | OSCC | ribonucleoprotein complex biogenesis | 333/7305 | 463/18723 | 8.28e-48 | 5.24e-44 | 333 |
GO:000838020 | Oral cavity | OSCC | RNA splicing | 308/7305 | 434/18723 | 2.43e-42 | 7.70e-39 | 308 |
GO:000037519 | Oral cavity | OSCC | RNA splicing, via transesterification reactions | 225/7305 | 324/18723 | 5.20e-29 | 2.99e-26 | 225 |
GO:000037719 | Oral cavity | OSCC | RNA splicing, via transesterification reactions with bulged adenosine as nucleophile | 221/7305 | 320/18723 | 5.50e-28 | 2.18e-25 | 221 |
GO:000039819 | Oral cavity | OSCC | mRNA splicing, via spliceosome | 221/7305 | 320/18723 | 5.50e-28 | 2.18e-25 | 221 |
GO:007182620 | Oral cavity | OSCC | ribonucleoprotein complex subunit organization | 152/7305 | 227/18723 | 1.05e-17 | 1.01e-15 | 152 |
GO:002261820 | Oral cavity | OSCC | ribonucleoprotein complex assembly | 146/7305 | 220/18723 | 1.53e-16 | 1.23e-14 | 146 |
GO:005109820 | Oral cavity | OSCC | regulation of binding | 212/7305 | 363/18723 | 3.88e-14 | 2.15e-12 | 212 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
GEMIN2 | SNV | Missense_Mutation | rs771609900 | c.635N>A | p.Gly212Glu | p.G212E | O14893 | protein_coding | deleterious(0.04) | probably_damaging(0.94) | TCGA-A8-A09C-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
GEMIN2 | SNV | Missense_Mutation | novel | c.175N>C | p.Glu59Gln | p.E59Q | O14893 | protein_coding | deleterious(0) | possibly_damaging(0.874) | TCGA-AQ-A7U7-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Targeted Molecular therapy | rituximab | CR |
GEMIN2 | SNV | Missense_Mutation | c.191C>T | p.Pro64Leu | p.P64L | O14893 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-E9-A229-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
GEMIN2 | SNV | Missense_Mutation | rs752769842 | c.674N>T | p.Pro225Leu | p.P225L | O14893 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-2W-A8YY-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
GEMIN2 | SNV | Missense_Mutation | novel | c.653N>C | p.Leu218Ser | p.L218S | O14893 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CM-6674-01 | Colorectum | colon adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD |
GEMIN2 | SNV | Missense_Mutation | novel | c.341G>A | p.Arg114Gln | p.R114Q | O14893 | protein_coding | deleterious(0.02) | probably_damaging(0.997) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
GEMIN2 | SNV | Missense_Mutation | rs775884653 | c.479N>A | p.Gly160Glu | p.G160E | O14893 | protein_coding | tolerated(0.77) | benign(0.003) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
GEMIN2 | SNV | Missense_Mutation | novel | c.803N>T | p.Arg268Met | p.R268M | O14893 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AJ-A3EK-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Chemotherapy | carboplatin | CR |
GEMIN2 | SNV | Missense_Mutation | c.689C>T | p.Ala230Val | p.A230V | O14893 | protein_coding | tolerated(0.3) | benign(0.309) | TCGA-AP-A051-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
GEMIN2 | SNV | Missense_Mutation | c.233G>T | p.Arg78Met | p.R78M | O14893 | protein_coding | deleterious(0.01) | possibly_damaging(0.814) | TCGA-AX-A0J1-01 | 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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