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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for SQRDL |
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Phenotypic Information for SQRDL(metabolism pathway, cancer, disease, phenome) |
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Cancer | CGAP: SQRDL |
Familial Cancer Database: SQRDL |
* This gene is included in those cancer gene databases. |
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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/ |
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REACTOME_SULFUR_AMINO_ACID_METABOLISM REACTOME_METABOLISM_OF_AMINO_ACIDS_AND_DERIVATIVES |
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OMIM | |
Orphanet | |
Disease | KEGG Disease: SQRDL |
MedGen: SQRDL (Human Medical Genetics with Condition) | |
ClinVar: SQRDL | |
Phenotype | MGI: SQRDL (International Mouse Phenotyping Consortium) |
PhenomicDB: SQRDL |
Mutations for SQRDL |
* 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. |
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- Statistics for Tissue and Mutation type | Top |
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- For Inter-chromosomal Variations |
There's no inter-chromosomal structural variation. |
- For Intra-chromosomal Variations |
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'. |
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Sample | Symbol_a | Chr_a | Start_a | End_a | Symbol_b | Chr_b | Start_b | End_b |
ovary | SQRDL | chr15 | 45963439 | 45963459 | SQRDL | chr15 | 45963906 | 45963926 |
ovary | SQRDL | chr15 | 45975836 | 45975856 | chr15 | 46002144 | 46002164 |
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract) |
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* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows SQRDL 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 |
BU581446 | NID1 | 4 | 299 | 1 | 236143879 | 236148727 | SQRDL | 300 | 495 | 15 | 45981354 | 45983304 | |
BU075210 | SQRDL | 41 | 401 | 15 | 45981354 | 45983469 | NID1 | 402 | 583 | 1 | 236143879 | 236145017 |
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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) |
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Stat. for Non-Synonymous SNVs (# total SNVs=26) | (# total SNVs=9) |
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(# total SNVs=0) | (# total SNVs=0) |
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* 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 |
chr15:45965849-45965849 | p.S168S | 4 |
chr15:45981249-45981249 | p.T377A | 2 |
chr15:45951155-45951155 | p.R12fs*51 | 2 |
chr15:45965918-45965918 | p.I191M | 2 |
chr15:45968449-45968449 | p.D269N | 2 |
chr15:45968487-45968487 | p.P281P | 2 |
chr15:45951302-45951302 | p.R61C | 1 |
chr15:45974674-45974674 | p.? | 1 |
chr15:45965852-45965852 | p.N169K | 1 |
chr15:45981393-45981393 | p.L425L | 1 |
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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 |   | 2 |   |   | 3 |   | 2 |   |   | 6 |   | 1 |   | 1 | 11 | 1 |   | 6 |
# mutation |   | 2 |   | 2 |   |   | 3 |   | 2 |   |   | 7 |   | 1 |   | 1 | 11 | 1 |   | 6 |
nonsynonymous SNV |   | 2 |   | 2 |   |   | 2 |   | 1 |   |   | 6 |   | 1 |   |   | 6 | 1 |   | 3 |
synonymous SNV |   |   |   |   |   |   | 1 |   | 1 |   |   | 1 |   |   |   | 1 | 5 |   |   | 3 |
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]) |
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* 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 |
chr15:45965849 | p.S168S,SQRDL | 3 |
chr15:45954208 | p.R222Q,SQRDL | 1 |
chr15:45965918 | p.R442H,SQRDL | 1 |
chr15:45974710 | p.Y82S,SQRDL | 1 |
chr15:45954319 | p.K224E,SQRDL | 1 |
chr15:45965929 | p.S97F,SQRDL | 1 |
chr15:45974832 | p.A225S,SQRDL | 1 |
chr15:45962136 | p.E134G,SQRDL | 1 |
chr15:45965940 | p.R139L,SQRDL | 1 |
chr15:45974846 | p.G238W,SQRDL | 1 |
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* 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. |
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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] |
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Gene Expression for SQRDL |
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* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data. |
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* 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)) |
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* This plots show the correlation between CNV and gene expression. |
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Gene-Gene Network Information |
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* 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 |
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B2M,EMC7,RHOV___CHP1,CYB561D2,CYB5A,DNAJC17,FAH, RMDN3,FTH1,GCHFR,NDUFAF1,PPP1R7,RARRES3,SQRDL, TMEM62,TPST2,TSPAN15,UQCRQ,VPS18,YIPF1,ZFYVE19 | ARHGDIB,ARPC3,BCAS4,BRE,CAPZB,CLIC1,GSTO1, JTB,MFSD5,MIF4GD,N6AMT2,NPC2,PRR13,PSMA4, PSMA5,RHOG,RNF181,S100A11,SDHAF2,SQRDL,TM2D2 |
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ACADS,BCL10,GSKIP,C15orf48,CCL28,CIB1,ETFA, ETHE1,F2RL1,FAM118B,GPA33,LDHD,LGALS3,MPDU1, PIGR,RILP,SCO2,SQRDL,TMEM54,TNFSF13,TSPO | ATP5B,MCU,CCL28,CD24,CSTF2,GNG5,HCCS, HDAC1,HPSE,IL18,MAP2K6,MMAA,MYCBP,OSTF1, PSMD3,RAB11A,RTN4IP1,SCO1,SQRDL,TMEM54,TPM3 |
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* 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 |
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Pharmacological Information for SQRDL |
There's no related Drug. |
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Cross referenced IDs for SQRDL |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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