MyWEST - Mining Results

Differentially expressed gene list

MT_RA-4h.xls: excel file containing a list of 729 genes induced or repressed after 4 hours of 10^-6 M Retinoic Acid treatment of U937 hematopoietic precursor cells, which represent the test data set used in the validation of our system. Out of these 729 candidate regulated genes, 339 were induced and 390 repressed.

Tables of combined mined annotations

Each table is contained in a distinct excel file and is the result of a specific complex articulated query implemented in the database of the aggregated mined data.

• _MyRegulatedGenes.xls: expression regulations in the considered experiment, and gene symbols and titles of the testing genes. Out of the 729 identified candidate regulated genes, 513 (221 induced, 292 repressed) were classified genes and 216 (118 induced, 98 repressed) ESTs, according to the UniGene build Hs.160 - release 14 June 2003.
  
  
• A_ClusterID-Symbol&Title_UG.xls: comprehensive view of the expression regulations of the test data set and the UniGene cluster ID, gene symbol, and gene title annotations, mined from the UniGene web databank.
  
  
• A_CytogeneticLocation_LL.xls: comprehensive view of the expression regulations of the test data set and the cytogenetic location annotations, mined from the LocusLink web databank.
  
  
• A_Disorders&Mutations_GC.xls: comprehensive view of the expression regulations of the test data set and the disorder and mutation annotations, mined from the GeneCards web databank.
  
  
• A_FunctionalAnalysis-Transcription_LL_SP.xls: comprehensive integrated view of the expression regulations of the test data set and the functional analysis results presenting the transcription related genes (according to the Gene Ontology, RefSeq Summary, Gene Reference Into Function, keyword, and function annotations mined from the LocusLink and Swiss-Prot web databanks, respectively).
  
  
• A_FunctionalAnalysis-Differentiation_LL_SP.xls: comprehensive integrated view of the expression regulations of the test data set and the functional analysis results presenting the differentiation related genes (according to the Gene Ontology, RefSeq Summary, Gene Reference Into Function, keyword, and function annotations mined from the LocusLink and Swiss-Prot web databanks, respectively).
  
  
• A_GeneOntology_LL.xls: comprehensive view of the expression regulations of the test data set and the Gene Ontology functional categories, mined from the LocusLink web databank.
  
  
• A_GeneRIF_LL.xls: comprehensive view of the expression regulations of the test data set and the Gene Reference Into Function annotations, mined from the LocusLink web databank.
  
  
• A_GenomeWideResources_SS_GC.xls: comprehensive integrated view of the expression regulations of the test data setand the reference codes in several resources, mined from the SOURCE and GeneCards web databanks.
  
  
• A_GenomicContig-Ortholog-EC_Number_LL_SS.xls: comprehensive integrated view of the expression regulations of the test data set and the genomic contig reference codes, mouse ortholog reference codes, and EC numbers, mined from the LocusLink and SOURCE web databanks.
  
  
• A_Keywords_SP.xls: comprehensive view of the expression regulations of the test data set and the protein product keywords, mined from the Swiss-Prot web databank.
  
  
• A_mRNASequences_UG.xls: comprehensive view of the expression regulations of the test data set and the mRNA sequence reference codes, mined from the UniGene web databank.
  
  
• A_Name&Origin-SequenceInformation_SP.xls: comprehensive view of the expression regulations of the test data set and the protein product names, origins, molecular weights, and lengths, mined from the Swiss-Prot web databank.
  
  
• A_NormalizedExpression_SS.xls: comprehensive view of the expression regulations of the test data set and the normalized expressions in different tissues, mined from the SOURCE web databank.
  
  
• A_OverviewRefSeqSummary_LL.xls: comprehensive view of the expression regulations of the test data set and the functional RefSeq Summary annotations, mined from the LocusLink web databank.
  
  
• A_Phenotype_LL.xls: comprehensive view of the expression regulations of the test data set and the phenotype annotations, mined from the LocusLink web databank.
  
  
• A_ProteinSimilarities_UG.xls: comprehensive view of the expression regulations of the test data set and the protein product similarities in different organisms - with the percent identity and length of the aligned regions - mined from the UniGene web databank.
  
  
• A_RefSeq_LL.xls: comprehensive view of the expression regulations of the test data set and the genomic contig and mRNA Reference Sequence codes, mined from the LocusLink web databank.
  
  
• A_SwissProtInfo-Disease_SP.xls: comprehensive view of the expression regulations of the test data set and the disease annotations, mined from the Swiss-Prot web databank.
  
  
• A_SwissProtInfo-Function_SP.xls: comprehensive view of the expression regulations of the test data set and the function annotations, mined from the Swiss-Prot web databank.
  
  
• A_SwissProtInfo-ProteinExpression_SP.xls: comprehensive view of the expression regulations of the test data set and the protein product expression annotations - including tissue specificity, developmental stage, and induction - mined from the Swiss-Prot web databank.
  
  
• A_SwissProtInfo-ProteinFunction_SP.xls: comprehensive view of the expression regulations of the test data set and the protein product functional annotations - including pathway, function, subcellular location, enzyme regulation, catalytic activity, and cofactor - mined from the Swiss-Prot web databank.
  
  
• A_SwissProtInfo-ProteinStructure_SP.xls: comprehensive view of the expression regulations of the test data set and the protein product structure annotations - including domain, similarity, ptm, subunit, and polymorphism - mined from the Swiss-Prot web databank.