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Gene: LRP1 |
Gene summary for LRP1 |
Gene summary. |
Gene information | Species | Human | Gene symbol | LRP1 | Gene ID | 4035 |
Gene name | LDL receptor related protein 1 | |
Gene Alias | A2MR | |
Cytomap | 12q13.3 | |
Gene Type | protein-coding | GO ID | GO:0000165 | UniProtAcc | Q07954 |
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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 |
4035 | LRP1 | P74T-E | Human | Esophagus | ESCC | 1.05e-11 | 2.93e-01 | 0.1479 |
4035 | LRP1 | P75T-E | Human | Esophagus | ESCC | 1.16e-06 | 2.02e-01 | 0.1125 |
4035 | LRP1 | P76T-E | Human | Esophagus | ESCC | 7.17e-05 | 5.02e-02 | 0.1207 |
4035 | LRP1 | P79T-E | Human | Esophagus | ESCC | 2.08e-11 | 1.60e-01 | 0.1154 |
4035 | LRP1 | P80T-E | Human | Esophagus | ESCC | 4.57e-11 | 7.62e-02 | 0.155 |
4035 | LRP1 | P82T-E | Human | Esophagus | ESCC | 8.74e-06 | 3.27e-01 | 0.1072 |
4035 | LRP1 | P83T-E | Human | Esophagus | ESCC | 1.60e-05 | 2.60e-01 | 0.1738 |
4035 | LRP1 | P89T-E | Human | Esophagus | ESCC | 5.70e-11 | 1.10e+00 | 0.1752 |
4035 | LRP1 | P91T-E | Human | Esophagus | ESCC | 7.48e-13 | 1.54e+00 | 0.1828 |
4035 | LRP1 | P104T-E | Human | Esophagus | ESCC | 6.92e-10 | 3.88e-01 | 0.0931 |
4035 | LRP1 | P107T-E | Human | Esophagus | ESCC | 4.11e-24 | 7.40e-01 | 0.171 |
4035 | LRP1 | P126T-E | Human | Esophagus | ESCC | 2.83e-04 | 1.01e-01 | 0.1125 |
4035 | LRP1 | P127T-E | Human | Esophagus | ESCC | 2.39e-15 | 1.59e-02 | 0.0826 |
4035 | LRP1 | P128T-E | Human | Esophagus | ESCC | 9.13e-11 | 6.26e-01 | 0.1241 |
4035 | LRP1 | P130T-E | Human | Esophagus | ESCC | 2.75e-18 | 4.77e-01 | 0.1676 |
4035 | LRP1 | NAFLD1 | Human | Liver | NAFLD | 6.83e-10 | 7.08e-01 | -0.04 |
4035 | LRP1 | S41 | Human | Liver | Cirrhotic | 5.84e-04 | 6.26e-01 | -0.0343 |
4035 | LRP1 | S43 | Human | Liver | Cirrhotic | 1.71e-11 | 4.06e-01 | -0.0187 |
4035 | LRP1 | HCC1_Meng | Human | Liver | HCC | 1.79e-69 | 2.02e-01 | 0.0246 |
4035 | LRP1 | HCC2_Meng | Human | Liver | HCC | 5.32e-17 | 8.72e-03 | 0.0107 |
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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:004217610 | Cervix | CC | regulation of protein catabolic process | 104/2311 | 391/18723 | 9.39e-15 | 9.36e-12 | 104 |
GO:001081010 | Cervix | CC | regulation of cell-substrate adhesion | 69/2311 | 221/18723 | 8.57e-14 | 5.69e-11 | 69 |
GO:00315898 | Cervix | CC | cell-substrate adhesion | 96/2311 | 363/18723 | 1.48e-13 | 8.85e-11 | 96 |
GO:005254710 | Cervix | CC | regulation of peptidase activity | 112/2311 | 461/18723 | 6.70e-13 | 3.08e-10 | 112 |
GO:190336210 | Cervix | CC | regulation of cellular protein catabolic process | 72/2311 | 255/18723 | 5.98e-12 | 2.10e-09 | 72 |
GO:003297010 | Cervix | CC | regulation of actin filament-based process | 96/2311 | 397/18723 | 4.00e-11 | 8.54e-09 | 96 |
GO:004573210 | Cervix | CC | positive regulation of protein catabolic process | 65/2311 | 231/18723 | 7.44e-11 | 1.39e-08 | 65 |
GO:190382910 | Cervix | CC | positive regulation of cellular protein localization | 72/2311 | 276/18723 | 3.20e-10 | 4.46e-08 | 72 |
GO:01501159 | Cervix | CC | cell-substrate junction organization | 37/2311 | 101/18723 | 3.20e-10 | 4.46e-08 | 37 |
GO:007265910 | Cervix | CC | protein localization to plasma membrane | 73/2311 | 284/18723 | 4.95e-10 | 6.73e-08 | 73 |
GO:000989610 | Cervix | CC | positive regulation of catabolic process | 109/2311 | 492/18723 | 5.26e-10 | 6.99e-08 | 109 |
GO:003295610 | Cervix | CC | regulation of actin cytoskeleton organization | 86/2311 | 358/18723 | 5.90e-10 | 7.51e-08 | 86 |
GO:00070448 | Cervix | CC | cell-substrate junction assembly | 34/2311 | 95/18723 | 3.35e-09 | 3.45e-07 | 34 |
GO:00160557 | Cervix | CC | Wnt signaling pathway | 98/2311 | 444/18723 | 4.82e-09 | 4.65e-07 | 98 |
GO:00321035 | Cervix | CC | positive regulation of response to external stimulus | 95/2311 | 427/18723 | 5.44e-09 | 5.03e-07 | 95 |
GO:01987387 | Cervix | CC | cell-cell signaling by wnt | 98/2311 | 446/18723 | 6.16e-09 | 5.58e-07 | 98 |
GO:19907788 | Cervix | CC | protein localization to cell periphery | 78/2311 | 333/18723 | 1.22e-08 | 9.73e-07 | 78 |
GO:00019528 | Cervix | CC | regulation of cell-matrix adhesion | 40/2311 | 128/18723 | 1.32e-08 | 1.04e-06 | 40 |
GO:00071608 | Cervix | CC | cell-matrix adhesion | 60/2311 | 233/18723 | 1.58e-08 | 1.23e-06 | 60 |
GO:00071626 | Cervix | CC | negative regulation of cell adhesion | 72/2311 | 303/18723 | 2.36e-08 | 1.70e-06 | 72 |
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Enriched KEGG pathways. |
Pathway ID | Tissue | Disease Stage | Description | Gene Ratio | Bg Ratio | pvalue | p.adjust | qvalue | Count |
hsa0501018 | Cervix | CC | Alzheimer disease | 113/1267 | 384/8465 | 9.67e-14 | 3.92e-12 | 2.32e-12 | 113 |
hsa0501019 | Cervix | CC | Alzheimer disease | 113/1267 | 384/8465 | 9.67e-14 | 3.92e-12 | 2.32e-12 | 113 |
hsa05010 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
hsa050101 | Colorectum | AD | Alzheimer disease | 174/2092 | 384/8465 | 1.82e-19 | 9.26e-18 | 5.91e-18 | 174 |
hsa050102 | Colorectum | SER | Alzheimer disease | 146/1580 | 384/8465 | 6.52e-20 | 2.40e-18 | 1.75e-18 | 146 |
hsa050103 | Colorectum | SER | Alzheimer disease | 146/1580 | 384/8465 | 6.52e-20 | 2.40e-18 | 1.75e-18 | 146 |
hsa050104 | Colorectum | MSS | Alzheimer disease | 169/1875 | 384/8465 | 1.21e-22 | 1.01e-20 | 6.21e-21 | 169 |
hsa050105 | Colorectum | MSS | Alzheimer disease | 169/1875 | 384/8465 | 1.21e-22 | 1.01e-20 | 6.21e-21 | 169 |
hsa050108 | Colorectum | FAP | Alzheimer disease | 105/1404 | 384/8465 | 3.74e-08 | 1.04e-06 | 6.33e-07 | 105 |
hsa050109 | Colorectum | FAP | Alzheimer disease | 105/1404 | 384/8465 | 3.74e-08 | 1.04e-06 | 6.33e-07 | 105 |
hsa05010210 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
hsa0501038 | Esophagus | ESCC | Alzheimer disease | 263/4205 | 384/8465 | 1.80e-14 | 5.47e-13 | 2.80e-13 | 263 |
hsa049796 | Liver | NAFLD | Cholesterol metabolism | 20/1043 | 51/8465 | 9.73e-07 | 4.56e-05 | 3.67e-05 | 20 |
hsa0497911 | Liver | NAFLD | Cholesterol metabolism | 20/1043 | 51/8465 | 9.73e-07 | 4.56e-05 | 3.67e-05 | 20 |
hsa0501014 | Liver | Cirrhotic | Alzheimer disease | 180/2530 | 384/8465 | 5.52e-13 | 1.36e-11 | 8.36e-12 | 180 |
hsa049792 | Liver | Cirrhotic | Cholesterol metabolism | 30/2530 | 51/8465 | 1.59e-05 | 1.39e-04 | 8.60e-05 | 30 |
hsa0501015 | Liver | Cirrhotic | Alzheimer disease | 180/2530 | 384/8465 | 5.52e-13 | 1.36e-11 | 8.36e-12 | 180 |
hsa049793 | Liver | Cirrhotic | Cholesterol metabolism | 30/2530 | 51/8465 | 1.59e-05 | 1.39e-04 | 8.60e-05 | 30 |
hsa0501022 | Liver | HCC | Alzheimer disease | 254/4020 | 384/8465 | 3.75e-14 | 8.97e-13 | 4.99e-13 | 254 |
hsa049794 | Liver | HCC | Cholesterol metabolism | 41/4020 | 51/8465 | 1.33e-06 | 1.35e-05 | 7.49e-06 | 41 |
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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 |
MDK | LRP1 | MDK_LRP1 | MK | Breast | DCIS |
MDK | LRP1 | MDK_LRP1 | MK | Breast | Healthy |
MDK | LRP1 | MDK_LRP1 | MK | Breast | IDC |
MDK | LRP1 | MDK_LRP1 | MK | Breast | Precancer |
MDK | LRP1 | MDK_LRP1 | MK | Cervix | ADJ |
MDK | LRP1 | MDK_LRP1 | MK | Cervix | CC |
MDK | LRP1 | MDK_LRP1 | MK | Cervix | Healthy |
MDK | LRP1 | MDK_LRP1 | MK | Cervix | Precancer |
MDK | LRP1 | MDK_LRP1 | MK | CRC | AD |
MDK | LRP1 | MDK_LRP1 | MK | CRC | ADJ |
MDK | LRP1 | MDK_LRP1 | MK | CRC | MSI-H |
MDK | LRP1 | MDK_LRP1 | MK | CRC | MSS |
MDK | LRP1 | MDK_LRP1 | MK | CRC | SER |
MDK | LRP1 | MDK_LRP1 | MK | Endometrium | ADJ |
MDK | LRP1 | MDK_LRP1 | MK | Endometrium | AEH |
MDK | LRP1 | MDK_LRP1 | MK | Endometrium | EEC |
MDK | LRP1 | MDK_LRP1 | MK | Endometrium | Healthy |
MDK | LRP1 | MDK_LRP1 | MK | Esophagus | ESCC |
MDK | LRP1 | MDK_LRP1 | MK | Esophagus | Healthy |
MDK | LRP1 | MDK_LRP1 | MK | GC | ADJ |
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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 |
LRP1 | SNV | Missense_Mutation | novel | c.1064N>A | p.Gly355Glu | p.G355E | Q07954 | protein_coding | deleterious(0) | probably_damaging(0.998) | TCGA-A1-A0SH-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | tc | SD |
LRP1 | SNV | Missense_Mutation | rs769600453 | c.11248N>T | p.Arg3750Trp | p.R3750W | Q07954 | protein_coding | deleterious(0.01) | possibly_damaging(0.545) | TCGA-A1-A0SN-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | ac | SD |
LRP1 | SNV | Missense_Mutation | rs748577199 | c.2461N>C | p.Thr821Pro | p.T821P | Q07954 | protein_coding | tolerated(0.06) | benign(0.276) | TCGA-A2-A0CS-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Hormone Therapy | anastrozole | SD |
LRP1 | SNV | Missense_Mutation | c.8327C>T | p.Pro2776Leu | p.P2776L | Q07954 | protein_coding | tolerated(0.08) | benign(0.049) | TCGA-A2-A1G4-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Chemotherapy | adriamycin | SD | |
LRP1 | SNV | Missense_Mutation | c.13037G>T | p.Arg4346Leu | p.R4346L | Q07954 | protein_coding | tolerated(0.14) | benign(0.069) | TCGA-A2-A25A-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Unspecific | Cytoxan | SD | |
LRP1 | SNV | Missense_Mutation | novel | c.2440N>C | p.Cys814Arg | p.C814R | Q07954 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-A2-A3Y0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
LRP1 | SNV | Missense_Mutation | novel | c.2441N>T | p.Cys814Phe | p.C814F | Q07954 | protein_coding | deleterious(0) | probably_damaging(0.986) | TCGA-A2-A3Y0-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | adriamycin | CR |
LRP1 | SNV | Missense_Mutation | c.4843G>A | p.Asp1615Asn | p.D1615N | Q07954 | protein_coding | deleterious(0.03) | probably_damaging(0.985) | TCGA-A8-A076-01 | Breast | breast invasive carcinoma | Female | >=65 | I/II | Hormone Therapy | anastrozole | SD | |
LRP1 | SNV | Missense_Mutation | rs761146982 | c.5119N>G | p.Leu1707Val | p.L1707V | Q07954 | protein_coding | deleterious(0.05) | probably_damaging(0.967) | TCGA-A8-A08L-01 | Breast | breast invasive carcinoma | Female | >=65 | III/IV | Unknown | Unknown | SD |
LRP1 | SNV | Missense_Mutation | c.13606N>A | p.Glu4536Lys | p.E4536K | Q07954 | protein_coding | deleterious(0.01) | benign(0.034) | TCGA-A8-A095-01 | Breast | breast invasive carcinoma | Female | <65 | I/II | Chemotherapy | 5-fluorouracil | CR |
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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 |
4035 | LRP1 | KINASE, DRUGGABLE GENOME | ANTISENSE OLIGONUCLEOTIDES | 11095961 |
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