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Gene: GRIN1 |
Gene summary for GRIN1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | GRIN1 | Gene ID | 2902 |
Gene name | glutamate ionotropic receptor NMDA type subunit 1 | |
Gene Alias | GluN1 | |
Cytomap | 9q34.3 | |
Gene Type | protein-coding | GO ID | GO:0001101 | UniProtAcc | Q05586 |
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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 |
2902 | GRIN1 | HTA11_78_2000001011 | Human | Colorectum | AD | 5.21e-05 | 2.88e-01 | -0.1088 |
2902 | GRIN1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.20e-05 | 3.46e-01 | -0.1207 |
2902 | GRIN1 | HTA11_696_2000001011 | Human | Colorectum | AD | 4.08e-11 | 2.87e-01 | -0.1464 |
2902 | GRIN1 | HTA11_866_2000001011 | Human | Colorectum | AD | 8.62e-04 | 1.32e-01 | -0.1001 |
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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:0045862 | Colorectum | AD | positive regulation of proteolysis | 129/3918 | 372/18723 | 4.04e-10 | 3.46e-08 | 129 |
GO:2000116 | Colorectum | AD | regulation of cysteine-type endopeptidase activity | 79/3918 | 235/18723 | 3.74e-06 | 1.03e-04 | 79 |
GO:0052547 | Colorectum | AD | regulation of peptidase activity | 137/3918 | 461/18723 | 4.12e-06 | 1.12e-04 | 137 |
GO:0010952 | Colorectum | AD | positive regulation of peptidase activity | 68/3918 | 197/18723 | 6.30e-06 | 1.59e-04 | 68 |
GO:0052548 | Colorectum | AD | regulation of endopeptidase activity | 124/3918 | 432/18723 | 6.58e-05 | 1.07e-03 | 124 |
GO:0010950 | Colorectum | AD | positive regulation of endopeptidase activity | 59/3918 | 179/18723 | 1.11e-04 | 1.65e-03 | 59 |
GO:0009410 | Colorectum | AD | response to xenobiotic stimulus | 128/3918 | 462/18723 | 2.69e-04 | 3.31e-03 | 128 |
GO:0072593 | Colorectum | AD | reactive oxygen species metabolic process | 73/3918 | 239/18723 | 2.79e-04 | 3.42e-03 | 73 |
GO:2000379 | Colorectum | AD | positive regulation of reactive oxygen species metabolic process | 29/3918 | 76/18723 | 4.31e-04 | 4.82e-03 | 29 |
GO:2001056 | Colorectum | AD | positive regulation of cysteine-type endopeptidase activity | 47/3918 | 148/18723 | 1.30e-03 | 1.14e-02 | 47 |
GO:2000377 | Colorectum | AD | regulation of reactive oxygen species metabolic process | 48/3918 | 157/18723 | 2.77e-03 | 2.09e-02 | 48 |
GO:0097305 | Colorectum | AD | response to alcohol | 71/3918 | 253/18723 | 4.01e-03 | 2.80e-02 | 71 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa05010 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
hsa05016 | Colorectum | AD | Huntington disease | 147/2092 | 306/8465 | 1.93e-19 | 9.26e-18 | 5.91e-18 | 147 |
hsa05020 | Colorectum | AD | Prion disease | 133/2092 | 273/8465 | 2.47e-18 | 8.29e-17 | 5.29e-17 | 133 |
hsa05014 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
hsa05022 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
hsa05017 | Colorectum | AD | Spinocerebellar ataxia | 60/2092 | 143/8465 | 3.78e-06 | 4.35e-05 | 2.78e-05 | 60 |
hsa04015 | Colorectum | AD | Rap1 signaling pathway | 71/2092 | 210/8465 | 1.72e-03 | 9.68e-03 | 6.18e-03 | 71 |
hsa04720 | Colorectum | AD | Long-term potentiation | 26/2092 | 67/8465 | 7.26e-03 | 2.97e-02 | 1.89e-02 | 26 |
hsa050101 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
hsa050161 | Colorectum | AD | Huntington disease | 147/2092 | 306/8465 | 1.93e-19 | 9.26e-18 | 5.91e-18 | 147 |
hsa050201 | Colorectum | AD | Prion disease | 133/2092 | 273/8465 | 2.47e-18 | 8.29e-17 | 5.29e-17 | 133 |
hsa050141 | Colorectum | AD | Amyotrophic lateral sclerosis | 164/2092 | 364/8465 | 4.28e-18 | 1.27e-16 | 8.09e-17 | 164 |
hsa050221 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
hsa050171 | Colorectum | AD | Spinocerebellar ataxia | 60/2092 | 143/8465 | 3.78e-06 | 4.35e-05 | 2.78e-05 | 60 |
hsa040151 | Colorectum | AD | Rap1 signaling pathway | 71/2092 | 210/8465 | 1.72e-03 | 9.68e-03 | 6.18e-03 | 71 |
hsa047201 | Colorectum | AD | Long-term potentiation | 26/2092 | 67/8465 | 7.26e-03 | 2.97e-02 | 1.89e-02 | 26 |
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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 |
GRIN1 | SNV | Missense_Mutation | c.473N>G | p.Tyr158Cys | p.Y158C | Q05586 | protein_coding | deleterious(0) | possibly_damaging(0.908) | TCGA-CK-4951-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
GRIN1 | SNV | Missense_Mutation | c.2435C>T | p.Thr812Met | p.T812M | Q05586 | protein_coding | tolerated(0.08) | possibly_damaging(0.609) | TCGA-G4-6588-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
GRIN1 | SNV | Missense_Mutation | c.888N>T | p.Lys296Asn | p.K296N | Q05586 | protein_coding | tolerated(0.29) | benign(0.043) | TCGA-F5-6814-01 | Colorectum | rectum adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
GRIN1 | insertion | Frame_Shift_Ins | novel | c.2364dupC | p.Trp789LeufsTer32 | p.W789Lfs*32 | Q05586 | protein_coding | TCGA-CM-4743-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Chemotherapy | capecitabine | SD | ||
GRIN1 | SNV | Missense_Mutation | novel | c.206N>T | p.Pro69Leu | p.P69L | Q05586 | protein_coding | tolerated(0.06) | benign(0.102) | TCGA-A5-A0G2-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
GRIN1 | SNV | Missense_Mutation | novel | c.446N>C | p.Ser149Thr | p.S149T | Q05586 | protein_coding | tolerated(0.16) | benign(0.015) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
GRIN1 | SNV | Missense_Mutation | rs797044925 | c.2506N>A | p.Gly836Arg | p.G836R | Q05586 | protein_coding | deleterious(0) | probably_damaging(0.993) | TCGA-A5-A1OF-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
GRIN1 | SNV | Missense_Mutation | novel | c.622N>T | p.Arg208Cys | p.R208C | Q05586 | protein_coding | deleterious(0.05) | probably_damaging(0.953) | TCGA-A5-A2K5-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
GRIN1 | SNV | Missense_Mutation | rs767651510 | c.2762N>T | p.Thr921Met | p.T921M | Q05586 | protein_coding | deleterious_low_confidence(0.01) | benign(0.01) | TCGA-AP-A059-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
GRIN1 | SNV | Missense_Mutation | novel | c.679N>A | p.Ala227Thr | p.A227T | Q05586 | protein_coding | tolerated(0.29) | benign(0.001) | TCGA-AX-A2HC-01 | Endometrium | uterine corpus endometrioid carcinoma | Female | <65 | III/IV | Chemotherapy | paclitaxel | PD |
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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 |
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | DIZOCILPINE | DIZOCILPINE | 20361801 | |
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | antagonist | CHEMBL3545351 | AV-101 | |
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | methamphetamine | METHAMPHETAMINE | 23880023 | |
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | antagonist | CHEMBL2068724 | ACAMPROSATE CALCIUM | |
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | PHILANTHOTOXIN 343 | PHILANTHOTOXIN 343 | 20873775 | |
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | antagonist | CHEMBL2068839 | RISLENEMDAZ | |
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | antagonist | CHEMBL1569 | AMANTADINE HYDROCHLORIDE | |
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | KETAMINE | KETAMINE | 20361801 | |
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | V3381 | INDANTADOL | ||
2902 | GRIN1 | ION CHANNEL, DRUGGABLE GENOME, CELL SURFACE | antagonist | CHEMBL2107771 | RALFINAMIDE |
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