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Gene: GRIN2D |
Gene summary for GRIN2D |
 Gene summary. |
| 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 |
| 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 |
| 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 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| 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 |
| ∗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: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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| 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 |
| 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 |
| 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 |
| GRIN2D | SNV | Missense_Mutation | c.2609N>G | p.Tyr870Cys | p.Y870C | O15399 | protein_coding | deleterious(0.03) | benign(0.021) | TCGA-A8-A09Z-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GRIN2D | SNV | Missense_Mutation | c.1363T>C | p.Cys455Arg | p.C455R | O15399 | protein_coding | deleterious(0) | probably_damaging(0.996) | TCGA-AO-A128-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| GRIN2D | SNV | Missense_Mutation | c.2542G>A | p.Val848Ile | p.V848I | O15399 | protein_coding | deleterious(0) | possibly_damaging(0.855) | TCGA-AR-A1AO-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | doxorubicin | SD | |
| GRIN2D | SNV | Missense_Mutation | c.2500N>A | p.Glu834Lys | p.E834K | O15399 | protein_coding | deleterious(0.04) | probably_damaging(0.996) | TCGA-E2-A1B5-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | tamoxiphen | SD | |
| GRIN2D | SNV | Missense_Mutation | rs369036985 | c.1067N>A | p.Arg356His | p.R356H | O15399 | protein_coding | tolerated(0.14) | possibly_damaging(0.511) | TCGA-C5-A3HD-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | SD |
| GRIN2D | SNV | Missense_Mutation | c.505N>A | p.Glu169Lys | p.E169K | O15399 | protein_coding | tolerated(0.15) | benign(0.187) | TCGA-IR-A3LI-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR | |
| GRIN2D | SNV | Missense_Mutation | novel | c.1763N>C | p.Met588Thr | p.M588T | O15399 | protein_coding | deleterious(0) | possibly_damaging(0.516) | TCGA-VS-A9UD-01 | Cervix | cervical & endocervical cancer | Female | >=65 | III/IV | Chemotherapy | cisplatin | CR |
| GRIN2D | SNV | Missense_Mutation | c.2564C>T | p.Ala855Val | p.A855V | O15399 | protein_coding | deleterious(0) | benign(0.191) | TCGA-A6-A565-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unspecific | 5FU | PD | |
| GRIN2D | SNV | Missense_Mutation | c.2620N>T | p.Arg874Trp | p.R874W | O15399 | protein_coding | deleterious(0) | probably_damaging(0.972) | TCGA-AA-3710-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
| GRIN2D | SNV | Missense_Mutation | c.652N>T | p.Arg218Cys | p.R218C | O15399 | protein_coding | tolerated(0.06) | probably_damaging(0.981) | TCGA-AA-3842-01 | Colorectum | colon adenocarcinoma | Male | <65 | III/IV | Chemotherapy | folinic | 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 |
| 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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