search for: kinase

Dear all, Here is my code which am using to combine 5th column from different data sets. Here is the function to do my job genesymbol.append.file <-NULL gene.column <- NULL readGeneSymbol <- function(files,genesymbol.column=5){ for(i in fnames){ temp <- read.table(fnames,header=T,sep="\t",stringsAsFactors=F,quote="\"")

Hi, I have the following data frame: > print(mydatframe) __DATAFRAME__ V1 V2 V3 1 1007_s_at DDR1 discoidin domain receptor tyrosine kinase 1 2 1053_at RFC2 replication factor C (activator 1) 2, 40kDa 3 117_at HSPA6 heat shock 70kDa protein 6 (HSP70B') __END__ Is there a way to create a hash with V2 as Key and V3 as its value? - Gundala Viswanath Jakarta - Indonesia

Hi, I have the following data file to be parsed and captured as a data frame: __DATA__ #GDS_ID GENE_NAME GENE_DESCRIPTION GENE_FUNCTION 1007_s_at | DDR1 | discoidin domain receptor tyrosine kinase 1 | protein-coding 1053_at | RFC2 | replication factor C (activator 1) 2, 40kDa | protein-coding 117_at | HSPA6 | heat shock 70kDa protein 6 (HSP70B') | protein-coding __END__ In particular it is separated by " | " , namely - space, bar, space. However I tried this without avail: g...

...501174632e-06,"IMP- 171597 171597 KOG1347 Uncharacterized membrane protein, predicted efflux pump General function prediction only POORLY CHARACTERIZED 171658 171658 KOG4290 Predicted membrane protein Function unknown POORLY CHARACTERIZED 171660 171660 KOG0903 Phosphatidylinositol 4-kinase, involved in intracellular trafficking and secretion Signal transduction mechanisms CELLULAR 171660 171660 KOG0903 Phosphatidylinositol 4-kinase, involved in intracellular trafficking and secretion Intracellular trafficking, secretion, and 171703 171703 KOG2674 Cysteine protease required for...

...wing lines, 08248-GOTERM 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process 08279-GOTERM 3'-phosphoadenosine 5'-phosphosulfate binding 08494-GOTERM 'de novo' posttranslational protein folding 08712-GOTERM ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity 08759-GOTERM double-stranded DNA specific 5'-3' exodeoxyribonuclease activity 09127-GOTERM 'de novo' actin filament nucleation 09180-GOTERM 5'-tyrosyl-DNA phosphodiesterase activity 09282-GOTERM deoxyribonucleoside 5'-monophosphate N-glycosidase activity...

Hello, The 179th and 180th elements of my list of lists look like this: [[179]] [[179]]$desc [1] ">ipi|IPI00646510|IPI00646510.2 ISOFORM P60-HCK OF TYROSINE-PROTEIN KINASE HCK." [[179]]$seq [1] "MGGRSSCEDPGCPRDEERAPRMGCMKSKFLQVGGNTFSKTETSASPHCPVYVPDPTSTIKPGPNSHNSNTP GIREAGSEDIIVVALYDYEAIHHEDLSFQKGDQMVVLEESGEWWKARSLATRKEGYIPSNYVARVDSLETEE WFFKGISRKDAERQLLAPGNMLGSFMIRDSETTKGSYSLSVRDYDPRQGDTVKHYKIRTLDNGGFYISPRST FSTLQELVDHYKKGNDGLCQKLSVPCMSSKPQKPWEKDAWEIP...

...E DATA (http://bioinformatics.nki.nl/vacancies.php) THREE BIOINFORMATICS POSITIONS PROJECT OUTLINE Genomic alterations are major determinant of responses to (targeted) therapies in cancer. In fact, the best positive and negative predictors of responses to targeted therapies are alterations in kinases or their direct downstream effectors. To gain insight into resistance mechanisms to therapy and thus better tailor treatment, we are approaching this problem from two different angles. First, we have acquired large panels of human tumors, on which we are currently performing kinase exon sequencing...

...8248-GOTERM 3'-phosphoadenosine 5'-phosphosulfate biosynthetic process > 08279-GOTERM 3'-phosphoadenosine 5'-phosphosulfate binding > 08494-GOTERM 'de novo' posttranslational protein folding > 08712-GOTERM ATP-dependent polyribonucleotide 5'-hydroxyl-kinase activity > 08759-GOTERM double-stranded DNA specific 5'-3' exodeoxyribonuclease activity > 09127-GOTERM 'de novo' actin filament nucleation > 09180-GOTERM 5'-tyrosyl-DNA phosphodiesterase activity > 09282-GOTERM deoxyribonucleoside 5'-monophosphate N-...

...Synaptic transmission,Protein targeting,Small molecule transport,Exocytosis, A_51_P100309 NM_001039652.1 Opioid receptor,Mu opioid receptor,GPCRs rhodopsin-like superfamily,GPCRs rhodopsin-like G-PROTEIN COUPLED RECEPTOR,INTERACTOR PROTEIN FOR CYTOHESIN EXCHANGE FACTORS 1,CONNECTOR ENCHANCER OF KINASE SUPPRESSOR OF RAS,MU-TYPE OPIOID RECEPTOR (MOR-1) Neuronal activities,Signal transduction,Sensory perception,Biological process unclassified Synaptic transmission,Pain sensation,Cell surface receptor mediated signal transduction A_51_P100327 NM_013683.1 ABC transporter-like,APOBEC/CMP deaminas...

...hich an example can be seen here: http://rcytoscape.systemsbiology.net/versions/current/gallery/TCGA/subnet.TCGA.02.0014.png This portrays 1) gene expression (green: under-expression; red: over-expression) 2) copy number (blue: high, black: low) 3) gene type (node shape: hexagons are kinases, arrows are ligands, diamonds are receptors, circles for everything else) 4) mutation status (not SNPs, but non-synonymous amino acid substitutions) 5) in the context of gene relationships, from KEGG A vignette for a larger version of this network is nearly complete. The Cytoscape networ...