|
Gene: LRP5 |
Gene summary for LRP5 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LRP5 | Gene ID | 4041 |
Gene name | LDL receptor related protein 5 | |
Gene Alias | BMND1 | |
Cytomap | 11q13.2 | |
Gene Type | protein-coding | GO ID | GO:0000278 | UniProtAcc | O75197 |
Top |
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 |
4041 | LRP5 | HTA11_3410_2000001011 | Human | Colorectum | AD | 4.25e-02 | 2.23e-01 | 0.0155 |
4041 | LRP5 | HTA11_2487_2000001011 | Human | Colorectum | SER | 3.19e-02 | 3.05e-01 | -0.1808 |
4041 | LRP5 | HTA11_1938_2000001011 | Human | Colorectum | AD | 1.46e-04 | 4.35e-01 | -0.0811 |
4041 | LRP5 | HTA11_78_2000001011 | Human | Colorectum | AD | 1.61e-03 | 3.07e-01 | -0.1088 |
4041 | LRP5 | HTA11_347_2000001011 | Human | Colorectum | AD | 1.61e-12 | 5.14e-01 | -0.1954 |
4041 | LRP5 | HTA11_83_2000001011 | Human | Colorectum | SER | 9.33e-05 | 5.17e-01 | -0.1526 |
4041 | LRP5 | HTA11_696_2000001011 | Human | Colorectum | AD | 4.01e-14 | 6.69e-01 | -0.1464 |
4041 | LRP5 | HTA11_866_2000001011 | Human | Colorectum | AD | 1.75e-04 | 4.27e-01 | -0.1001 |
4041 | LRP5 | HTA11_1391_2000001011 | Human | Colorectum | AD | 1.13e-13 | 7.54e-01 | -0.059 |
4041 | LRP5 | HTA11_546_2000001011 | Human | Colorectum | AD | 2.07e-04 | 5.25e-01 | -0.0842 |
4041 | LRP5 | HTA11_866_3004761011 | Human | Colorectum | AD | 1.44e-02 | 2.88e-01 | 0.096 |
4041 | LRP5 | HTA11_7696_3000711011 | Human | Colorectum | AD | 6.19e-03 | 4.54e-01 | 0.0674 |
4041 | LRP5 | HTA11_6818_2000001011 | Human | Colorectum | AD | 1.32e-02 | 5.17e-01 | 0.0112 |
4041 | LRP5 | HTA11_6818_2000001021 | Human | Colorectum | AD | 4.22e-03 | 4.01e-01 | 0.0588 |
4041 | LRP5 | HTA11_99999971662_82457 | Human | Colorectum | MSS | 2.36e-02 | 5.05e-01 | 0.3859 |
4041 | LRP5 | HTA11_99999973899_84307 | Human | Colorectum | MSS | 1.63e-07 | 7.44e-01 | 0.2585 |
4041 | LRP5 | A015-C-203 | Human | Colorectum | FAP | 3.77e-14 | -1.75e-01 | -0.1294 |
4041 | LRP5 | A002-C-201 | Human | Colorectum | FAP | 3.94e-03 | -2.04e-02 | 0.0324 |
4041 | LRP5 | A001-C-108 | Human | Colorectum | FAP | 1.00e-06 | 7.70e-02 | -0.0272 |
4041 | LRP5 | A002-C-205 | Human | Colorectum | FAP | 1.85e-09 | -5.00e-02 | -0.1236 |
Page: 1 2 3 4 5 6 |
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. |
Top |
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:0048732 | Colorectum | AD | gland development | 149/3918 | 436/18723 | 6.07e-11 | 6.33e-09 | 149 |
GO:0009743 | Colorectum | AD | response to carbohydrate | 86/3918 | 253/18723 | 8.43e-07 | 2.90e-05 | 86 |
GO:0044282 | Colorectum | AD | small molecule catabolic process | 118/3918 | 376/18723 | 1.05e-06 | 3.55e-05 | 118 |
GO:0030879 | Colorectum | AD | mammary gland development | 53/3918 | 137/18723 | 1.46e-06 | 4.58e-05 | 53 |
GO:0043434 | Colorectum | AD | response to peptide hormone | 126/3918 | 414/18723 | 2.70e-06 | 7.86e-05 | 126 |
GO:0034284 | Colorectum | AD | response to monosaccharide | 76/3918 | 225/18723 | 4.64e-06 | 1.23e-04 | 76 |
GO:0016052 | Colorectum | AD | carbohydrate catabolic process | 56/3918 | 154/18723 | 7.01e-06 | 1.73e-04 | 56 |
GO:0033500 | Colorectum | AD | carbohydrate homeostasis | 84/3918 | 259/18723 | 9.10e-06 | 2.15e-04 | 84 |
GO:0009746 | Colorectum | AD | response to hexose | 73/3918 | 219/18723 | 1.20e-05 | 2.65e-04 | 73 |
GO:0010563 | Colorectum | AD | negative regulation of phosphorus metabolic process | 130/3918 | 442/18723 | 1.26e-05 | 2.76e-04 | 130 |
GO:0009749 | Colorectum | AD | response to glucose | 71/3918 | 212/18723 | 1.31e-05 | 2.85e-04 | 71 |
GO:0042593 | Colorectum | AD | glucose homeostasis | 83/3918 | 258/18723 | 1.44e-05 | 3.11e-04 | 83 |
GO:0001678 | Colorectum | AD | cellular glucose homeostasis | 60/3918 | 172/18723 | 1.49e-05 | 3.18e-04 | 60 |
GO:0016055 | Colorectum | AD | Wnt signaling pathway | 130/3918 | 444/18723 | 1.60e-05 | 3.37e-04 | 130 |
GO:0045936 | Colorectum | AD | negative regulation of phosphate metabolic process | 129/3918 | 441/18723 | 1.81e-05 | 3.76e-04 | 129 |
GO:0019318 | Colorectum | AD | hexose metabolic process | 77/3918 | 237/18723 | 1.96e-05 | 4.01e-04 | 77 |
GO:0198738 | Colorectum | AD | cell-cell signaling by wnt | 130/3918 | 446/18723 | 2.02e-05 | 4.10e-04 | 130 |
GO:0051348 | Colorectum | AD | negative regulation of transferase activity | 85/3918 | 268/18723 | 2.07e-05 | 4.19e-04 | 85 |
GO:0001667 | Colorectum | AD | ameboidal-type cell migration | 137/3918 | 475/18723 | 2.17e-05 | 4.33e-04 | 137 |
GO:0006066 | Colorectum | AD | alcohol metabolic process | 106/3918 | 353/18723 | 3.02e-05 | 5.57e-04 | 106 |
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 |
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 |
hsa05022 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
hsa05225 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
hsa04928 | Colorectum | AD | Parathyroid hormone synthesis, secretion and action | 38/2092 | 106/8465 | 6.60e-03 | 2.77e-02 | 1.76e-02 | 38 |
hsa04310 | Colorectum | AD | Wnt signaling pathway | 56/2092 | 171/8465 | 1.03e-02 | 3.93e-02 | 2.51e-02 | 56 |
hsa050101 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
hsa050221 | Colorectum | AD | Pathways of neurodegeneration - multiple diseases | 201/2092 | 476/8465 | 4.54e-18 | 1.27e-16 | 8.09e-17 | 201 |
hsa052251 | Colorectum | AD | Hepatocellular carcinoma | 59/2092 | 168/8465 | 1.50e-03 | 8.69e-03 | 5.54e-03 | 59 |
hsa049281 | Colorectum | AD | Parathyroid hormone synthesis, secretion and action | 38/2092 | 106/8465 | 6.60e-03 | 2.77e-02 | 1.76e-02 | 38 |
hsa043101 | Colorectum | AD | Wnt signaling pathway | 56/2092 | 171/8465 | 1.03e-02 | 3.93e-02 | 2.51e-02 | 56 |
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 |
hsa049282 | Colorectum | SER | Parathyroid hormone synthesis, secretion and action | 31/1580 | 106/8465 | 5.20e-03 | 3.28e-02 | 2.38e-02 | 31 |
hsa050103 | Colorectum | SER | Alzheimer disease | 146/1580 | 384/8465 | 6.52e-20 | 2.40e-18 | 1.75e-18 | 146 |
hsa050223 | Colorectum | SER | Pathways of neurodegeneration - multiple diseases | 168/1580 | 476/8465 | 6.23e-19 | 2.07e-17 | 1.50e-17 | 168 |
hsa049283 | Colorectum | SER | Parathyroid hormone synthesis, secretion and action | 31/1580 | 106/8465 | 5.20e-03 | 3.28e-02 | 2.38e-02 | 31 |
hsa050104 | Colorectum | MSS | Alzheimer disease | 169/1875 | 384/8465 | 1.21e-22 | 1.01e-20 | 6.21e-21 | 169 |
hsa050224 | Colorectum | MSS | Pathways of neurodegeneration - multiple diseases | 192/1875 | 476/8465 | 2.79e-20 | 1.04e-18 | 6.36e-19 | 192 |
hsa052252 | Colorectum | MSS | Hepatocellular carcinoma | 56/1875 | 168/8465 | 5.04e-04 | 3.45e-03 | 2.11e-03 | 56 |
hsa049284 | Colorectum | MSS | Parathyroid hormone synthesis, secretion and action | 37/1875 | 106/8465 | 1.72e-03 | 9.13e-03 | 5.59e-03 | 37 |
Page: 1 2 3 4 |
Top |
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 |
WNT7B | FZD4_LRP5 | WNT7B_FZD4_LRP5 | WNT | Cervix | ADJ |
WNT7B | FZD6_LRP5 | WNT7B_FZD6_LRP5 | WNT | Cervix | ADJ |
WNT2B | FZD6_LRP5 | WNT2B_FZD6_LRP5 | WNT | Cervix | CC |
WNT9A | FZD6_LRP5 | WNT9A_FZD6_LRP5 | WNT | Cervix | CC |
WNT4 | FZD5_LRP5 | WNT4_FZD5_LRP5 | WNT | CRC | AD |
WNT2 | FZD6_LRP5 | WNT2_FZD6_LRP5 | WNT | Endometrium | ADJ |
WNT4 | FZD6_LRP5 | WNT4_FZD6_LRP5 | WNT | Endometrium | ADJ |
WNT10A | FZD4_LRP5 | WNT10A_FZD4_LRP5 | WNT | HNSCC | OSCC |
WNT10A | FZD6_LRP5 | WNT10A_FZD6_LRP5 | WNT | HNSCC | OSCC |
WNT2 | FZD4_LRP5 | WNT2_FZD4_LRP5 | WNT | HNSCC | OSCC |
WNT2 | FZD6_LRP5 | WNT2_FZD6_LRP5 | WNT | HNSCC | OSCC |
WNT4 | FZD4_LRP5 | WNT4_FZD4_LRP5 | WNT | HNSCC | OSCC |
WNT4 | FZD6_LRP5 | WNT4_FZD6_LRP5 | WNT | HNSCC | OSCC |
WNT7B | FZD4_LRP5 | WNT7B_FZD4_LRP5 | WNT | HNSCC | OSCC |
WNT7B | FZD6_LRP5 | WNT7B_FZD6_LRP5 | WNT | HNSCC | OSCC |
WNT10A | FZD6_LRP5 | WNT10A_FZD6_LRP5 | WNT | HNSCC | Precancer |
WNT2 | FZD6_LRP5 | WNT2_FZD6_LRP5 | WNT | HNSCC | Precancer |
WNT2B | FZD6_LRP5 | WNT2B_FZD6_LRP5 | WNT | HNSCC | Precancer |
WNT4 | FZD6_LRP5 | WNT4_FZD6_LRP5 | WNT | HNSCC | Precancer |
WNT7B | FZD6_LRP5 | WNT7B_FZD6_LRP5 | WNT | HNSCC | Precancer |
Page: 1 |
Top |
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 |
Top |
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 |
LRP5 | SNV | Missense_Mutation | novel | c.3681N>G | p.Ile1227Met | p.I1227M | O75197 | protein_coding | deleterious(0.01) | probably_damaging(0.999) | TCGA-VS-A958-01 | Cervix | cervical & endocervical cancer | Female | <65 | I/II | Chemotherapy | cisplatin | CR |
LRP5 | SNV | Missense_Mutation | rs779534615 | c.4096N>A | p.Asp1366Asn | p.D1366N | O75197 | protein_coding | deleterious(0.01) | possibly_damaging(0.573) | TCGA-A6-2672-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
LRP5 | SNV | Missense_Mutation | rs765378705 | c.4226G>A | p.Arg1409His | p.R1409H | O75197 | protein_coding | deleterious(0) | probably_damaging(0.987) | TCGA-A6-2686-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD |
LRP5 | SNV | Missense_Mutation | c.1264G>A | p.Ala422Thr | p.A422T | O75197 | protein_coding | deleterious(0) | probably_damaging(0.997) | TCGA-AA-3811-01 | Colorectum | colon adenocarcinoma | Female | >=65 | III/IV | Unknown | Unknown | PD | |
LRP5 | SNV | Missense_Mutation | c.3082N>A | p.Asp1028Asn | p.D1028N | O75197 | protein_coding | deleterious(0) | probably_damaging(0.977) | TCGA-AA-3877-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
LRP5 | SNV | Missense_Mutation | novel | c.1204C>A | p.Leu402Met | p.L402M | O75197 | protein_coding | tolerated(0.08) | probably_damaging(0.913) | TCGA-AA-3947-01 | Colorectum | colon adenocarcinoma | Female | <65 | I/II | Unknown | Unknown | SD |
LRP5 | SNV | Missense_Mutation | c.4031N>T | p.Ala1344Val | p.A1344V | O75197 | protein_coding | tolerated(0.16) | possibly_damaging(0.523) | TCGA-AD-A5EJ-01 | Colorectum | colon adenocarcinoma | Female | >=65 | I/II | Unknown | Unknown | SD | |
LRP5 | SNV | Missense_Mutation | rs376164225 | c.4247C>T | p.Ala1416Val | p.A1416V | O75197 | protein_coding | tolerated(0.29) | benign(0.069) | TCGA-AZ-4615-01 | Colorectum | colon adenocarcinoma | Male | >=65 | III/IV | Chemotherapy | xeloda | PD |
LRP5 | SNV | Missense_Mutation | c.3329N>A | p.Gly1110Asp | p.G1110D | O75197 | protein_coding | tolerated(0.57) | benign(0.045) | TCGA-AZ-6601-01 | Colorectum | colon adenocarcinoma | Male | >=65 | I/II | Unknown | Unknown | PD | |
LRP5 | SNV | Missense_Mutation | c.1427C>A | p.Thr476Lys | p.T476K | O75197 | protein_coding | deleterious(0) | probably_damaging(0.968) | TCGA-CK-4948-01 | Colorectum | colon adenocarcinoma | Female | <65 | III/IV | Unknown | Unknown | SD |
Page: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 |
Top |
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 |