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Gene: NRXN1 |
Gene summary for NRXN1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NRXN1 | Gene ID | 9378 |
| Gene name | neurexin 1 | |
| Gene Alias | Hs.22998 | |
| Cytomap | 2p16.3 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q9ULB1 |
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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 |
| 9378 | NRXN1 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.63e-03 | 2.37e-01 | -0.0811 |
| 9378 | NRXN1 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.07e-05 | 2.03e-01 | -0.1954 |
| 9378 | NRXN1 | HTA11_2112_2000001011 | Human | Colorectum | SER | 3.11e-02 | 3.39e-01 | -0.2196 |
| 9378 | NRXN1 | HTA11_3361_2000001011 | Human | Colorectum | AD | 1.05e-06 | 2.92e-01 | -0.1207 |
| 9378 | NRXN1 | HTA11_696_2000001011 | Human | Colorectum | AD | 1.31e-10 | 3.13e-01 | -0.1464 |
| 9378 | NRXN1 | HTA11_866_2000001011 | Human | Colorectum | AD | 6.03e-04 | 2.00e-01 | -0.1001 |
| 9378 | NRXN1 | HTA11_1391_2000001011 | Human | Colorectum | AD | 8.13e-13 | 3.27e-01 | -0.059 |
| 9378 | NRXN1 | HTA11_5212_2000001011 | Human | Colorectum | AD | 2.27e-02 | 2.52e-01 | -0.2061 |
| 9378 | NRXN1 | HTA11_546_2000001011 | Human | Colorectum | AD | 2.76e-04 | 2.32e-01 | -0.0842 |
| 9378 | NRXN1 | HTA11_99999965062_69753 | Human | Colorectum | MSI-H | 1.09e-03 | 5.57e-01 | 0.3487 |
| 9378 | NRXN1 | HTA12-15-2 | Human | Pancreas | PDAC | 2.97e-13 | 9.78e-01 | 0.2315 |
| 9378 | NRXN1 | HTA12-23-1 | Human | Pancreas | PDAC | 2.88e-24 | 1.70e+00 | 0.3405 |
| 9378 | NRXN1 | HTA12-25-1 | Human | Pancreas | PDAC | 3.81e-22 | 1.55e+00 | 0.313 |
| 9378 | NRXN1 | HTA12-26-1 | Human | Pancreas | PDAC | 2.71e-57 | 1.96e+00 | 0.3728 |
| 9378 | NRXN1 | HTA12-29-1 | Human | Pancreas | PDAC | 8.43e-121 | 1.97e+00 | 0.3722 |
| 9378 | NRXN1 | HTA12-30-1 | Human | Pancreas | PDAC | 3.11e-06 | 1.61e+00 | 0.3671 |
| 9378 | NRXN1 | HTA12-32-1 | Human | Pancreas | PDAC | 1.97e-13 | 1.73e+00 | 0.3624 |
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| 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:0034329 | Colorectum | AD | cell junction assembly | 136/3918 | 420/18723 | 2.02e-08 | 1.15e-06 | 136 |
| GO:0007409 | Colorectum | AD | axonogenesis | 122/3918 | 418/18723 | 3.36e-05 | 6.15e-04 | 122 |
| GO:0061564 | Colorectum | AD | axon development | 132/3918 | 467/18723 | 8.40e-05 | 1.31e-03 | 132 |
| GO:0071709 | Colorectum | AD | membrane assembly | 22/3918 | 50/18723 | 2.00e-04 | 2.66e-03 | 22 |
| GO:0044091 | Colorectum | AD | membrane biogenesis | 22/3918 | 55/18723 | 9.88e-04 | 9.28e-03 | 22 |
| GO:1901888 | Colorectum | AD | regulation of cell junction assembly | 61/3918 | 204/18723 | 1.50e-03 | 1.27e-02 | 61 |
| GO:0099173 | Colorectum | AD | postsynapse organization | 51/3918 | 168/18723 | 2.47e-03 | 1.90e-02 | 51 |
| GO:0050808 | Colorectum | AD | synapse organization | 112/3918 | 426/18723 | 4.25e-03 | 2.92e-02 | 112 |
| GO:1902414 | Colorectum | AD | protein localization to cell junction | 31/3918 | 94/18723 | 4.30e-03 | 2.95e-02 | 31 |
| GO:0007411 | Colorectum | AD | axon guidance | 64/3918 | 227/18723 | 5.41e-03 | 3.55e-02 | 64 |
| GO:0050807 | Colorectum | AD | regulation of synapse organization | 60/3918 | 211/18723 | 5.67e-03 | 3.64e-02 | 60 |
| GO:0097485 | Colorectum | AD | neuron projection guidance | 64/3918 | 228/18723 | 6.02e-03 | 3.78e-02 | 64 |
| GO:00343291 | Colorectum | SER | cell junction assembly | 100/2897 | 420/18723 | 4.23e-06 | 1.61e-04 | 100 |
| GO:00717091 | Colorectum | SER | membrane assembly | 20/2897 | 50/18723 | 2.45e-05 | 6.84e-04 | 20 |
| GO:00991731 | Colorectum | SER | postsynapse organization | 46/2897 | 168/18723 | 5.20e-05 | 1.25e-03 | 46 |
| GO:00440911 | Colorectum | SER | membrane biogenesis | 20/2897 | 55/18723 | 1.21e-04 | 2.49e-03 | 20 |
| GO:00074111 | Colorectum | SER | axon guidance | 51/2897 | 227/18723 | 3.29e-03 | 2.82e-02 | 51 |
| GO:00974851 | Colorectum | SER | neuron projection guidance | 51/2897 | 228/18723 | 3.61e-03 | 3.03e-02 | 51 |
| GO:00615641 | Colorectum | SER | axon development | 94/2897 | 467/18723 | 3.78e-03 | 3.13e-02 | 94 |
| GO:19018881 | Colorectum | SER | regulation of cell junction assembly | 46/2897 | 204/18723 | 4.70e-03 | 3.70e-02 | 46 |
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| Enriched KEGG pathways. |
| Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
| Page: 1 |
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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 |
| NRXN1 | NLGN1 | NRXN1_NLGN1 | NRXN | CRC | ADJ |
| NRXN1 | NLGN1 | NRXN1_NLGN1 | NRXN | Endometrium | ADJ |
| NRXN1 | NLGN1 | NRXN1_NLGN1 | NRXN | GC | ADJ |
| NRXN1 | NLGN1 | NRXN1_NLGN1 | NRXN | Skin | SCCIS |
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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 |
| NRXN1 | SNV | Missense_Mutation | c.263N>A | p.Arg88His | p.R88H | Q9ULB1 | protein_coding | tolerated(0.3) | benign(0.067) | TCGA-A2-A3XS-01 | Breast | breast invasive carcinoma | Female | <65 | III/IV | Chemotherapy | cytoxan | PD | |
| NRXN1 | SNV | Missense_Mutation | c.1157C>T | p.Ala386Val | p.A386V | Q9ULB1 | protein_coding | tolerated(0.28) | possibly_damaging(0.634) | TCGA-A8-A06R-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| NRXN1 | SNV | Missense_Mutation | c.4595N>G | p.Lys1532Arg | p.K1532R | Q9ULB1 | protein_coding | deleterious(0.01) | benign(0.39) | TCGA-A8-A08G-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR | |
| NRXN1 | SNV | Missense_Mutation | c.4361N>C | p.Arg1454Thr | p.R1454T | Q9ULB1 | protein_coding | tolerated_low_confidence(0.05) | benign(0.009) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| NRXN1 | SNV | Missense_Mutation | novel | c.1889N>A | p.Ser630Tyr | p.S630Y | Q9ULB1 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-AN-A046-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| NRXN1 | SNV | Missense_Mutation | c.553N>T | p.Arg185Cys | p.R185C | Q9ULB1 | protein_coding | deleterious(0.05) | possibly_damaging(0.683) | TCGA-AN-A0AM-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NRXN1 | SNV | Missense_Mutation | c.3565N>A | p.Ala1189Thr | p.A1189T | Q9ULB1 | protein_coding | tolerated(0.63) | benign(0.015) | TCGA-AN-A0FY-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | |
| NRXN1 | SNV | Missense_Mutation | novel | c.3021T>A | p.Asp1007Glu | p.D1007E | Q9ULB1 | protein_coding | deleterious(0) | probably_damaging(0.947) | TCGA-AQ-A54N-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
| NRXN1 | SNV | Missense_Mutation | novel | c.1241N>A | p.Gly414Asp | p.G414D | Q9ULB1 | protein_coding | deleterious(0.01) | probably_damaging(0.947) | TCGA-BH-A0B8-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Hormone Therapy | arimidex | SD |
| NRXN1 | SNV | Missense_Mutation | c.692N>A | p.Gly231Glu | p.G231E | Q9ULB1 | protein_coding | deleterious(0.01) | probably_damaging(0.984) | TCGA-BH-A0DX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxotere | CR |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 |
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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 |
| 9378 | NRXN1 | CELL SURFACE, ION CHANNEL, DRUGGABLE GENOME, TRANSPORTER | antipsychotics | |||
| 9378 | NRXN1 | CELL SURFACE, ION CHANNEL, DRUGGABLE GENOME, TRANSPORTER | duloxetine | DULOXETINE | 29407288 |
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