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Gene: NLGN1 |
Gene summary for NLGN1 |
 Gene summary. |
| Gene information | Species | Human | Gene symbol | NLGN1 | Gene ID | 22871 |
| Gene name | neuroligin 1 | |
| Gene Alias | NL1 | |
| Cytomap | 3q26.31 | |
| Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | Q8N2Q7 |
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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 |
| 22871 | NLGN1 | AEH-subject4 | Human | Endometrium | AEH | 1.59e-14 | 6.13e-01 | -0.2657 |
| 22871 | NLGN1 | HTA12-15-2 | Human | Pancreas | PDAC | 2.08e-13 | 8.84e-01 | 0.2315 |
| 22871 | NLGN1 | HTA12-23-1 | Human | Pancreas | PDAC | 7.33e-25 | 1.62e+00 | 0.3405 |
| 22871 | NLGN1 | HTA12-25-1 | Human | Pancreas | PDAC | 9.43e-22 | 1.26e+00 | 0.313 |
| 22871 | NLGN1 | HTA12-26-1 | Human | Pancreas | PDAC | 5.37e-48 | 1.80e+00 | 0.3728 |
| 22871 | NLGN1 | HTA12-29-1 | Human | Pancreas | PDAC | 1.48e-110 | 1.82e+00 | 0.3722 |
| 22871 | NLGN1 | HTA12-30-1 | Human | Pancreas | PDAC | 1.14e-02 | 9.41e-01 | 0.3671 |
| 22871 | NLGN1 | HTA12-32-1 | Human | Pancreas | PDAC | 9.72e-12 | 1.48e+00 | 0.3624 |
| 22871 | NLGN1 | HTA12-9-2 | Human | Pancreas | PDAC | 2.11e-03 | 3.76e-01 | 0.0835 |
| Page: 1 |
| Transcriptomic changes along malignancy continuum. |
| Tissue | Expression Dynamics | Abbreviation |
| Endometrium |  | AEH: Atypical endometrial hyperplasia |
| EEC: Endometrioid 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:00485119 | Endometrium | AEH | rhythmic process | 67/2100 | 298/18723 | 1.69e-08 | 1.04e-06 | 67 |
| GO:000660516 | Endometrium | AEH | protein targeting | 68/2100 | 314/18723 | 6.30e-08 | 3.38e-06 | 68 |
| GO:00516568 | Endometrium | AEH | establishment of organelle localization | 77/2100 | 390/18723 | 4.89e-07 | 1.94e-05 | 77 |
| GO:00076239 | Endometrium | AEH | circadian rhythm | 47/2100 | 210/18723 | 2.54e-06 | 7.28e-05 | 47 |
| GO:00343299 | Endometrium | AEH | cell junction assembly | 78/2100 | 420/18723 | 4.80e-06 | 1.24e-04 | 78 |
| GO:00301009 | Endometrium | AEH | regulation of endocytosis | 44/2100 | 211/18723 | 3.39e-05 | 6.05e-04 | 44 |
| GO:00109758 | Endometrium | AEH | regulation of neuron projection development | 75/2100 | 445/18723 | 2.01e-04 | 2.54e-03 | 75 |
| GO:001003816 | Endometrium | AEH | response to metal ion | 65/2100 | 373/18723 | 2.02e-04 | 2.54e-03 | 65 |
| GO:00458078 | Endometrium | AEH | positive regulation of endocytosis | 24/2100 | 100/18723 | 2.27e-04 | 2.75e-03 | 24 |
| GO:00163588 | Endometrium | AEH | dendrite development | 46/2100 | 243/18723 | 2.56e-04 | 3.03e-03 | 46 |
| GO:19000275 | Endometrium | AEH | regulation of ruffle assembly | 11/2100 | 31/18723 | 3.44e-04 | 3.80e-03 | 11 |
| GO:00313468 | Endometrium | AEH | positive regulation of cell projection organization | 61/2100 | 353/18723 | 3.91e-04 | 4.20e-03 | 61 |
| GO:19018887 | Endometrium | AEH | regulation of cell junction assembly | 39/2100 | 204/18723 | 5.94e-04 | 5.86e-03 | 39 |
| GO:00971786 | Endometrium | AEH | ruffle assembly | 13/2100 | 44/18723 | 7.79e-04 | 7.36e-03 | 13 |
| GO:00516507 | Endometrium | AEH | establishment of vesicle localization | 32/2100 | 161/18723 | 8.99e-04 | 8.24e-03 | 32 |
| GO:00069035 | Endometrium | AEH | vesicle targeting | 13/2100 | 45/18723 | 9.84e-04 | 8.90e-03 | 13 |
| GO:00315296 | Endometrium | AEH | ruffle organization | 15/2100 | 56/18723 | 9.88e-04 | 8.90e-03 | 15 |
| GO:00427527 | Endometrium | AEH | regulation of circadian rhythm | 25/2100 | 121/18723 | 1.79e-03 | 1.43e-02 | 25 |
| GO:00308658 | Endometrium | AEH | cortical cytoskeleton organization | 15/2100 | 61/18723 | 2.50e-03 | 1.87e-02 | 15 |
| GO:00508086 | Endometrium | AEH | synapse organization | 67/2100 | 426/18723 | 2.67e-03 | 1.94e-02 | 67 |
| Page: 1 2 |
| 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 |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | CRC | AD |
| NRXN1 | NLGN1 | NRXN1_NLGN1 | NRXN | CRC | ADJ |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | CRC | ADJ |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | CRC | CRC |
| NRXN1 | NLGN1 | NRXN1_NLGN1 | NRXN | Endometrium | ADJ |
| NRXN2 | NLGN1 | NRXN2_NLGN1 | NRXN | Endometrium | ADJ |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | Endometrium | ADJ |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | Endometrium | AEH |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | Endometrium | EEC |
| NRXN2 | NLGN1 | NRXN2_NLGN1 | NRXN | Esophagus | ESCC |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | Esophagus | ESCC |
| NRXN1 | NLGN1 | NRXN1_NLGN1 | NRXN | GC | ADJ |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | GC | ADJ |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | HNSCC | Precancer |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | Lung | ADJ |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | Skin | ADJ |
| NRXN1 | NLGN1 | NRXN1_NLGN1 | NRXN | Skin | SCCIS |
| NRXN3 | NLGN1 | NRXN3_NLGN1 | NRXN | Skin | SCCIS |
| 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 |
| NLGN1 | SNV | Missense_Mutation | c.451G>A | p.Glu151Lys | p.E151K | Q8N2Q7 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-A7-A13E-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Targeted Molecular therapy | bevacizumab | PD | |
| NLGN1 | SNV | Missense_Mutation | c.1333N>A | p.Asp445Asn | p.D445N | Q8N2Q7 | protein_coding | tolerated(0.1) | possibly_damaging(0.523) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| NLGN1 | SNV | Missense_Mutation | c.2251N>C | p.Glu751Gln | p.E751Q | Q8N2Q7 | protein_coding | tolerated_low_confidence(0.12) | possibly_damaging(0.521) | TCGA-AC-A23H-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | PD | |
| NLGN1 | SNV | Missense_Mutation | c.2465N>C | p.Arg822Thr | p.R822T | Q8N2Q7 | protein_coding | deleterious_low_confidence(0) | probably_damaging(0.943) | TCGA-E9-A1RH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | SD | |
| NLGN1 | SNV | Missense_Mutation | c.1756N>A | p.Leu586Ile | p.L586I | Q8N2Q7 | protein_coding | tolerated(0.06) | possibly_damaging(0.892) | TCGA-GM-A2DH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | taxol | CR | |
| NLGN1 | insertion | In_Frame_Ins | novel | c.2151_2152insCTTTGG | p.Thr717_Thr718insLeuTrp | p.T717_T718insLW | Q8N2Q7 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| NLGN1 | insertion | Nonsense_Mutation | novel | c.2153_2154insCTGTGATTGATGGTGATGTAA | p.Thr718_Thr719insCysAspTerTrpTerCysAsn | p.T718_T719insCD*W*CN | Q8N2Q7 | protein_coding | TCGA-AN-A0FX-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unknown | Unknown | SD | ||
| NLGN1 | insertion | Nonsense_Mutation | novel | c.2320_2321insTTTAA | p.Pro774LeufsTer2 | p.P774Lfs*2 | Q8N2Q7 | protein_coding | TCGA-AR-A0TU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Doxorubicin | SD | ||
| NLGN1 | insertion | Frame_Shift_Ins | novel | c.2321_2322insT | p.Met776AsnfsTer52 | p.M776Nfs*52 | Q8N2Q7 | protein_coding | TCGA-AR-A0TU-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Doxorubicin | SD | ||
| NLGN1 | insertion | Nonsense_Mutation | novel | c.1444_1445insTCCTAACATTATATCATAGTTGAGAAACT | p.Pro482LeufsTer8 | p.P482Lfs*8 | Q8N2Q7 | protein_coding | TCGA-AR-A0U0-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
| Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 |
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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 |
| Page: 1 |
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