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Gene: GRIN2D |
Gene summary for GRIN2D |
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Gene information | Species | Human | Gene symbol | GRIN2D | Gene ID | 2906 |
Gene name | glutamate ionotropic receptor NMDA type subunit 2D | |
Gene Alias | DEE46 | |
Cytomap | 19q13.33 | |
Gene Type | protein-coding | GO ID | GO:0001964 | UniProtAcc | O15399 |
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Malignant transformation analysis |
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Entrez ID | Symbol | Replicates | Species | Organ | Tissue | Adj P-value | Log2FC | Malignancy |
2906 | GRIN2D | HTA11_3410_2000001011 | Human | Colorectum | AD | 1.11e-11 | 3.68e-01 | 0.0155 |
2906 | GRIN2D | HTA11_1938_2000001011 | Human | Colorectum | AD | 2.26e-14 | 5.50e-01 | -0.0811 |
2906 | GRIN2D | HTA11_78_2000001011 | Human | Colorectum | AD | 2.55e-06 | 2.92e-01 | -0.1088 |
2906 | GRIN2D | HTA11_83_2000001011 | Human | Colorectum | SER | 2.27e-03 | 3.46e-01 | -0.1526 |
2906 | GRIN2D | HTA11_696_2000001011 | Human | Colorectum | AD | 7.02e-04 | 1.50e-01 | -0.1464 |
2906 | GRIN2D | HTA11_1391_2000001011 | Human | Colorectum | AD | 3.76e-22 | 6.76e-01 | -0.059 |
2906 | GRIN2D | HTA11_546_2000001011 | Human | Colorectum | AD | 2.00e-03 | 3.34e-01 | -0.0842 |
2906 | GRIN2D | HTA11_10711_2000001011 | Human | Colorectum | AD | 1.09e-05 | 3.58e-01 | 0.0338 |
2906 | GRIN2D | HTA11_7696_3000711011 | Human | Colorectum | AD | 2.86e-21 | 5.72e-01 | 0.0674 |
2906 | GRIN2D | HTA11_6818_2000001021 | Human | Colorectum | AD | 3.40e-02 | 2.06e-01 | 0.0588 |
2906 | GRIN2D | HTA11_99999970781_79442 | Human | Colorectum | MSS | 8.77e-06 | 1.85e-01 | 0.294 |
2906 | GRIN2D | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.40e-04 | 7.94e-01 | 0.3487 |
2906 | GRIN2D | HTA11_99999965104_69814 | Human | Colorectum | MSS | 2.58e-04 | 3.37e-01 | 0.281 |
2906 | GRIN2D | HTA11_99999971662_82457 | Human | Colorectum | MSS | 5.34e-15 | 4.20e-01 | 0.3859 |
2906 | GRIN2D | HTA11_99999973899_84307 | Human | Colorectum | MSS | 5.93e-03 | 3.22e-01 | 0.2585 |
2906 | GRIN2D | CRC-3-11773 | Human | Colorectum | CRC | 1.09e-02 | 2.64e-01 | 0.2564 |
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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:0008344 | Colorectum | MSI-H | adult locomotory behavior | 13/1319 | 71/18723 | 1.24e-03 | 2.00e-02 | 13 |
GO:0050804 | Colorectum | CRC | modulation of chemical synaptic transmission | 70/2078 | 439/18723 | 1.15e-03 | 1.33e-02 | 70 |
GO:0099177 | Colorectum | CRC | regulation of trans-synaptic signaling | 70/2078 | 440/18723 | 1.23e-03 | 1.38e-02 | 70 |
GO:0042391 | Colorectum | CRC | regulation of membrane potential | 67/2078 | 434/18723 | 3.27e-03 | 2.81e-02 | 67 |
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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 |
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 |
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 |
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 |
hsa047201 | Colorectum | AD | Long-term potentiation | 26/2092 | 67/8465 | 7.26e-03 | 2.97e-02 | 1.89e-02 | 26 |
hsa050202 | Colorectum | SER | Prion disease | 119/1580 | 273/8465 | 4.61e-22 | 3.06e-20 | 2.22e-20 | 119 |
hsa050102 | Colorectum | SER | Alzheimer disease | 146/1580 | 384/8465 | 6.52e-20 | 2.40e-18 | 1.75e-18 | 146 |
hsa050222 | Colorectum | SER | Pathways of neurodegeneration - multiple diseases | 168/1580 | 476/8465 | 6.23e-19 | 2.07e-17 | 1.50e-17 | 168 |
hsa050142 | Colorectum | SER | Amyotrophic lateral sclerosis | 138/1580 | 364/8465 | 9.89e-19 | 2.99e-17 | 2.17e-17 | 138 |
hsa050172 | Colorectum | SER | Spinocerebellar ataxia | 46/1580 | 143/8465 | 6.78e-05 | 7.51e-04 | 5.45e-04 | 46 |
hsa047202 | Colorectum | SER | Long-term potentiation | 21/1580 | 67/8465 | 8.52e-03 | 4.26e-02 | 3.09e-02 | 21 |
hsa050203 | Colorectum | SER | Prion disease | 119/1580 | 273/8465 | 4.61e-22 | 3.06e-20 | 2.22e-20 | 119 |
hsa050103 | Colorectum | SER | Alzheimer disease | 146/1580 | 384/8465 | 6.52e-20 | 2.40e-18 | 1.75e-18 | 146 |
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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 |
GRIN2D | deletion | Frame_Shift_Del | c.1427delN | p.Arg478AlafsTer15 | p.R478Afs*15 | O15399 | protein_coding | TCGA-55-8207-01 | Lung | lung adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |||
GRIN2D | SNV | Missense_Mutation | novel | c.1859A>G | p.Lys620Arg | p.K620R | O15399 | protein_coding | tolerated(0.15) | probably_damaging(0.996) | TCGA-CR-6482-01 | Oral cavity | head & neck squamous cell carcinoma | Male | <65 | I/II | Chemotherapy | paclitaxel | SD |
GRIN2D | SNV | Missense_Mutation | c.907N>T | p.Gly303Trp | p.G303W | O15399 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-CV-7102-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
GRIN2D | SNV | Missense_Mutation | c.2500G>A | p.Glu834Lys | p.E834K | O15399 | protein_coding | deleterious(0.04) | probably_damaging(0.996) | TCGA-CV-7104-01 | Oral cavity | head & neck squamous cell carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
GRIN2D | SNV | Missense_Mutation | novel | c.2239N>G | p.Gln747Glu | p.Q747E | O15399 | protein_coding | tolerated(0.07) | benign(0.225) | TCGA-CV-A45P-01 | Oral cavity | head & neck squamous cell carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD |
GRIN2D | SNV | Missense_Mutation | rs752367785 | c.2182N>A | p.Asp728Asn | p.D728N | O15399 | protein_coding | tolerated(0.07) | possibly_damaging(0.47) | TCGA-CV-A6K2-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
GRIN2D | SNV | Missense_Mutation | novel | c.1987N>A | p.Ala663Thr | p.A663T | O15399 | protein_coding | deleterious(0) | probably_damaging(0.999) | TCGA-QK-A6VB-01 | Oral cavity | head & neck squamous cell carcinoma | Male | >=65 | I/II | Unknown | Unknown | PD |
GRIN2D | SNV | Missense_Mutation | novel | c.1700N>A | p.Arg567His | p.R567H | O15399 | protein_coding | deleterious(0) | probably_damaging(0.962) | TCGA-B7-A5TI-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | eloxatin | CR |
GRIN2D | SNV | Missense_Mutation | novel | c.3305N>T | p.Pro1102Leu | p.P1102L | O15399 | protein_coding | tolerated_low_confidence(0.12) | possibly_damaging(0.574) | TCGA-BR-8361-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
GRIN2D | SNV | Missense_Mutation | c.1436N>T | p.Pro479Leu | p.P479L | O15399 | protein_coding | tolerated(0.65) | benign(0.006) | TCGA-BR-8368-01 | 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 |
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | agonist | 178100907 | ||
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | CHEMBL2364609 | ESKETAMINE HYDROCHLORIDE | ||
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | antagonist | 178101060 | ||
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | blocker | 135652741 | ||
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | DIMIRACETAM | DIMIRACETAM | ||
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | antagonist | CHEMBL1200395 | ORPHENADRINE CITRATE | |
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | antagonist | CHEMBL1201023 | ORPHENADRINE HYDROCHLORIDE | |
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | antagonist | 178101025 | ||
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | agonist | 178101085 | N-METHYL-D-ASPARTIC ACID (NMDA) | |
2906 | GRIN2D | ION CHANNEL, DRUGGABLE GENOME | antagonist | 178100911 |
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