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Gene: LRP4 |
Gene summary for LRP4 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LRP4 | Gene ID | 4038 |
Gene name | LDL receptor related protein 4 | |
Gene Alias | CLSS | |
Cytomap | 11p11.2 | |
Gene Type | protein-coding | GO ID | GO:0000902 | UniProtAcc | O75096 |
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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 |
4038 | LRP4 | HTA11_3410_2000001011 | Human | Colorectum | AD | 6.55e-07 | 5.45e-01 | 0.0155 |
4038 | LRP4 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.32e-03 | 4.14e-01 | 0.096 |
4038 | LRP4 | HTA11_7696_3000711011 | Human | Colorectum | AD | 1.12e-26 | 1.35e+00 | 0.0674 |
4038 | LRP4 | HTA11_6818_2000001021 | Human | Colorectum | AD | 2.33e-02 | 5.97e-01 | 0.0588 |
4038 | LRP4 | HTA11_99999970781_79442 | Human | Colorectum | MSS | 7.12e-28 | 1.07e+00 | 0.294 |
4038 | LRP4 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 1.30e-11 | 1.26e+00 | 0.3859 |
4038 | LRP4 | A015-C-203 | Human | Colorectum | FAP | 1.56e-09 | -3.07e-03 | -0.1294 |
4038 | LRP4 | A001-C-119 | Human | Colorectum | FAP | 8.94e-43 | 1.21e+00 | -0.1557 |
4038 | LRP4 | A001-C-108 | Human | Colorectum | FAP | 8.30e-10 | 3.79e-01 | -0.0272 |
4038 | LRP4 | A002-C-021 | Human | Colorectum | FAP | 3.50e-04 | 4.88e-01 | 0.1171 |
4038 | LRP4 | A002-C-205 | Human | Colorectum | FAP | 5.06e-09 | 2.48e-01 | -0.1236 |
4038 | LRP4 | A001-C-104 | Human | Colorectum | FAP | 6.65e-09 | 4.93e-01 | 0.0184 |
4038 | LRP4 | A015-C-006 | Human | Colorectum | FAP | 4.96e-17 | 6.73e-01 | -0.0994 |
4038 | LRP4 | A015-C-106 | Human | Colorectum | FAP | 3.92e-06 | 2.41e-01 | -0.0511 |
4038 | LRP4 | A002-C-114 | Human | Colorectum | FAP | 2.65e-04 | 1.36e-01 | -0.1561 |
4038 | LRP4 | A015-C-104 | Human | Colorectum | FAP | 3.16e-13 | 5.19e-02 | -0.1899 |
4038 | LRP4 | A001-C-014 | Human | Colorectum | FAP | 4.45e-09 | 4.29e-01 | 0.0135 |
4038 | LRP4 | A002-C-016 | Human | Colorectum | FAP | 4.89e-08 | 1.58e-01 | 0.0521 |
4038 | LRP4 | A015-C-002 | Human | Colorectum | FAP | 4.37e-03 | 1.63e-01 | -0.0763 |
4038 | LRP4 | A001-C-203 | Human | Colorectum | FAP | 1.78e-05 | 3.18e-01 | -0.0481 |
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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:1903829 | Colorectum | AD | positive regulation of cellular protein localization | 110/3918 | 276/18723 | 4.58e-13 | 8.44e-11 | 110 |
GO:1905475 | Colorectum | AD | regulation of protein localization to membrane | 73/3918 | 175/18723 | 3.37e-10 | 2.93e-08 | 73 |
GO:0034329 | Colorectum | AD | cell junction assembly | 136/3918 | 420/18723 | 2.02e-08 | 1.15e-06 | 136 |
GO:1905477 | Colorectum | AD | positive regulation of protein localization to membrane | 46/3918 | 106/18723 | 1.47e-07 | 6.64e-06 | 46 |
GO:0030111 | Colorectum | AD | regulation of Wnt signaling pathway | 102/3918 | 328/18723 | 8.51e-06 | 2.03e-04 | 102 |
GO:0016055 | Colorectum | AD | Wnt signaling pathway | 130/3918 | 444/18723 | 1.60e-05 | 3.37e-04 | 130 |
GO:0198738 | Colorectum | AD | cell-cell signaling by wnt | 130/3918 | 446/18723 | 2.02e-05 | 4.10e-04 | 130 |
GO:0010975 | Colorectum | AD | regulation of neuron projection development | 129/3918 | 445/18723 | 2.88e-05 | 5.37e-04 | 129 |
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:0060070 | Colorectum | AD | canonical Wnt signaling pathway | 90/3918 | 303/18723 | 1.76e-04 | 2.38e-03 | 90 |
GO:0071709 | Colorectum | AD | membrane assembly | 22/3918 | 50/18723 | 2.00e-04 | 2.66e-03 | 22 |
GO:0060828 | Colorectum | AD | regulation of canonical Wnt signaling pathway | 77/3918 | 253/18723 | 2.19e-04 | 2.87e-03 | 77 |
GO:0031345 | Colorectum | AD | negative regulation of cell projection organization | 58/3918 | 186/18723 | 6.37e-04 | 6.58e-03 | 58 |
GO:0044091 | Colorectum | AD | membrane biogenesis | 22/3918 | 55/18723 | 9.88e-04 | 9.28e-03 | 22 |
GO:0050770 | Colorectum | AD | regulation of axonogenesis | 49/3918 | 154/18723 | 9.88e-04 | 9.28e-03 | 49 |
GO:0050767 | Colorectum | AD | regulation of neurogenesis | 99/3918 | 364/18723 | 2.35e-03 | 1.82e-02 | 99 |
GO:0099173 | Colorectum | AD | postsynapse organization | 51/3918 | 168/18723 | 2.47e-03 | 1.90e-02 | 51 |
GO:0010977 | Colorectum | AD | negative regulation of neuron projection development | 43/3918 | 137/18723 | 2.60e-03 | 1.97e-02 | 43 |
GO:0016358 | Colorectum | AD | dendrite development | 69/3918 | 243/18723 | 3.32e-03 | 2.42e-02 | 69 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
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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 |
LRP4 | SNV | Missense_Mutation | c.1022G>T | p.Ser341Ile | p.S341I | O75096 | protein_coding | deleterious(0.01) | benign(0.361) | TCGA-J9-A52C-01 | Prostate | prostate adenocarcinoma | Male | <65 | 9 | Unknown | Unknown | SD | |
LRP4 | SNV | Missense_Mutation | rs750691101 | c.3320N>A | p.Arg1107His | p.R1107H | O75096 | protein_coding | deleterious(0.01) | probably_damaging(0.994) | TCGA-M7-A725-01 | Prostate | prostate adenocarcinoma | Male | <65 | 7 | Unknown | Unknown | SD |
LRP4 | SNV | Missense_Mutation | novel | c.4629C>A | p.Asp1543Glu | p.D1543E | O75096 | protein_coding | deleterious(0.04) | probably_damaging(0.994) | TCGA-XK-AAIW-01 | Prostate | prostate adenocarcinoma | Male | >=65 | 9 | Unknown | Unknown | PD |
LRP4 | SNV | Missense_Mutation | c.3982N>T | p.Pro1328Ser | p.P1328S | O75096 | protein_coding | tolerated(0.12) | possibly_damaging(0.45) | TCGA-BR-6706-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Chemotherapy | 5-fluorouracil | PD | |
LRP4 | SNV | Missense_Mutation | c.4297C>A | p.Leu1433Met | p.L1433M | O75096 | protein_coding | deleterious(0.02) | probably_damaging(0.934) | TCGA-BR-8081-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
LRP4 | SNV | Missense_Mutation | c.863N>A | p.Arg288His | p.R288H | O75096 | protein_coding | tolerated(0.15) | probably_damaging(0.953) | TCGA-CD-5798-01 | Stomach | stomach adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | SD | |
LRP4 | SNV | Missense_Mutation | novel | c.1618N>A | p.Leu540Met | p.L540M | O75096 | protein_coding | deleterious(0.01) | probably_damaging(0.954) | TCGA-CG-5721-01 | Stomach | stomach adenocarcinoma | Male | <65 | III/IV | Unknown | Unknown | SD |
LRP4 | SNV | Missense_Mutation | c.5258N>G | p.Lys1753Arg | p.K1753R | O75096 | protein_coding | tolerated(0.24) | benign(0.076) | TCGA-D7-6526-01 | Stomach | stomach adenocarcinoma | Female | >=65 | III/IV | Chemotherapy | cisplatin | SD | |
LRP4 | SNV | Missense_Mutation | c.1730N>T | p.Pro577Leu | p.P577L | O75096 | protein_coding | deleterious(0) | probably_damaging(1) | TCGA-D7-8572-01 | Stomach | stomach adenocarcinoma | Male | <65 | I/II | Unknown | Unknown | SD | |
LRP4 | SNV | Missense_Mutation | c.814G>A | p.Ala272Thr | p.A272T | O75096 | protein_coding | tolerated(0.39) | benign(0.136) | TCGA-D7-A4YV-01 | Stomach | stomach adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
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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 |
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