|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for LDLRAP1 |
Top |
Phenotypic Information for LDLRAP1(metabolism pathway, cancer, disease, phenome) |
![]() | |
Cancer | CGAP: LDLRAP1 |
Familial Cancer Database: LDLRAP1 |
* This gene is included in those cancer gene databases. |
. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Oncogene 1 | Significant driver gene in |
cf) number; DB name 1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/, 3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html, 4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long, 5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php, 1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/ |
![]() | |
REACTOME_METABOLISM_OF_LIPIDS_AND_LIPOPROTEINS REACTOME_LIPOPROTEIN_METABOLISM |
Mutations for LDLRAP1 |
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site. |
![]() |
There's no structural variation information in COSMIC data for this gene. |
![]() |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows LDLRAP1 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
![]() |
Top |
![]() |
Mutation type/ Tissue ID | brca | cns | cerv | endome | haematopo | kidn | Lintest | liver | lung | ns | ovary | pancre | prost | skin | stoma | thyro | urina | |||
Total # sample |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   | |||
GAIN (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | |||
LOSS (# sample) |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract) |
Top |
![]() |
|
![]() |
Top |
![]() |
Stat. for Non-Synonymous SNVs (# total SNVs=16) | (# total SNVs=10) |
![]() | ![]() |
(# total SNVs=5) | (# total SNVs=2) |
![]() | ![]() |
Top |
![]() |
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID. |
GRCh37 position | Mutation(aa) | Unique sampleID count |
chr1:25889632-25889632 | p.S202fs*2 | 4 |
chr1:25880526-25880526 | p.A68S | 2 |
chr1:25893450-25893450 | p.S298S | 2 |
chr1:25889565-25889565 | p.K179K | 2 |
chr1:25889626-25889627 | p.S202fs*19 | 2 |
chr1:25890153-25890153 | p.L206F | 2 |
chr1:25891695-25891695 | p.S260L | 2 |
chr1:25883675-25883675 | p.D126N | 2 |
chr1:25883750-25883750 | p.R151G | 2 |
chr1:25880433-25880433 | p.D37Y | 1 |
Top |
![]() |
|
![]() |
Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 2 |   |   | 3 |   |   |   |   |   | 1 |   | 3 |   | 1 |   |   | 2 | 4 |   | 5 |
# mutation | 2 |   |   | 3 |   |   |   |   |   | 1 |   | 3 |   | 1 |   |   | 2 | 4 |   | 5 |
nonsynonymous SNV | 1 |   |   | 2 |   |   |   |   |   | 1 |   | 2 |   |   |   |   | 2 | 2 |   | 3 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   |   |   |   | 1 |   | 1 |   |   |   | 2 |   | 2 |
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma]) |
Top |
![]() |
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID. |
Genomic Position | Mutation(aa) | Unique sampleID count |
chr1:25891695 | p.S260L | 2 |
chr1:25880532 | p.R95Q | 1 |
chr1:25891685 | p.D126N | 1 |
chr1:25880543 | p.C143C | 1 |
chr1:25891690 | p.R151G | 1 |
chr1:25881403 | p.F171L | 1 |
chr1:25891691 | p.Q173R | 1 |
chr1:25883675 | p.L203L | 1 |
chr1:25883728 | p.E235K | 1 |
chr1:25893369 | p.P237S | 1 |
![]() |
![]() |
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene. |
![]() |
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma] |
Top |
Gene Expression for LDLRAP1 |
![]() |
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
![]() |
![]() |
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis. (t test, adjusted p<0.05 (using Benjamini-Hochberg FDR)) |
![]() |
Top |
![]() |
* This plots show the correlation between CNV and gene expression. |
![]() | |
![]() |
Top |
Gene-Gene Network Information |
![]() |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
![]() | |
AKR1A1,ATPIF1,CNKSR1,CTDSP1,MTFR1L,FAM73B,GPATCH3, GPN2,JMJD7-PLA2G4B,LDLRAP1,LYPLA2,LYPLA2P1,PEX14,PINK1, PQLC2,SEPN1,SYF2,TMEM222,TRAPPC12,ZBTB17,ZNF296 | APEX2,ARFIP2,C10orf35,SYNE4,CACFD1,CADM4,CLN3, DAK,DGCR2,DNAL4,ISYNA1,ITGA3,LDLRAP1,LPAR2, LSR,PAK4,PRKCZ,PRPF19,PRRG2,RAB17,SPINT2 |
![]() | |
ARHGEF10L,ATP13A2,KDF1,STPG1,CASP9,CASZ1,CLSTN1, DHDDS,DNAJC16,FUCA1,GALE,KIAA1522,LDLRAP1,LYPLA2, NBL1,PAFAH2,PQLC2,RPS6KA1,SLC44A4,TMEM57,TRIOBP | BDH1,CCNJL,CDX2,CPT2,DTX4,FUK,GOLPH3L, IHH,LDLRAP1,LGALS4,MB,NADK,SFXN5,SHD, SPR,STAP2,TRAF3IP2,TST,VAV3,WDR78,ZBTB7C |
![]() |
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown. Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene |
Top |
![]() |
Top |
Pharmacological Information for LDLRAP1 |
There's no related Drug. |
Top |
Cross referenced IDs for LDLRAP1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |