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Ely related to the specified biological process.ConclusionsWe have integrated heterogeneous
Ely related to the specified biological process.ConclusionsWe have integrated heterogeneous datasets to produce the first comprehensive functional gene network in D. melanogaster. We have shown that the functional relationships between genes are highly consistent with KEGG pathways1.8 and use these results to construct the two networks N 20 and 1.8 N 200 . We have demonstrated that edges drawn betweengene pairs are consistent with our biological expectation by revealing highly interconnected subnetworks of PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/28551822 genes that are nearly completely consistent with a common biological process. We also show how the network Tapinarof can be used to enhance the interpretation of microarray data by both discovering clusters of genes that are co-regulated and identifying candidate unannotated genes tightly coordinated with a known and co-regulated biological process. The full set of1.8 integrated data and networks built from these data ( N 20 and 1.8 N 200 ) are made available. We also provide GO:BP predic1.8 1.8 tions for 2,154 genes in N 20 and for 5,107 genes in N 200 .This community resource can be accessed online .Genome Biology 2009, 10:Rhttp://genomebiology.com/2009/10/9/RGenome Biology 2009,Volume 10, Issue 9, Article PubMed ID:https://www.ncbi.nlm.nih.gov/pubmed/26962111 RCostello et al. R97.Materials and methodsData acquisition, cleaning, normalization, filtering Genetic interactionsGIs were downloaded as a pre-computed file from FlyBase, version FB2007_02 . Interactions containing a gene not belonging to D. melanogaster were removed (that is, transgenic construct from D. simulans). All reported interactions (6,941) were given the same weight, a value of 1.The Affymetrix arrays were normalized using the Affy  and GCRMA  R packages. Affinities for all oligonucleotide sequences were calculated and the 'fullmodel' GCRMA normalization was run, resulting in log-transformed expression values for each probe set on each array. All spots or probe sets were mapped to the v5.3 D. melanogaster genome assembly and annotation. Genome sequence files were downloaded from FlyBase under the FB2007_02 release . Primer-based platforms required two rounds of BLAST; one round to match the primers to the genome (BLASTn; E-value < 10-2) and the second round to match the amplicon product to the genome (BLASTn; E-value < 10-6). Physical coordinates from the forward and reverse primers were checked for strandedness and to make sure the PCR product would be under 1,000 nucleotides. The segment of DNA between the forward and reverse primers (including the primers) was taken as the amplicon product for that primer pair and searched back against the genome to ensure the amplicon did not align to any other region outside the intended segment, potentially leading to cross-hybridization. cDNA-based arrays required the cDNA sequence be aligned against the genome to test for potential cross-hybridization. Any amplicons or cDNAs with a second best BLAST hit with 80 sequence identity were flagged and removed. Unique BLAST hits mapping to exons of v5.3 annotated genes were assigned the corresponding FlyBase gene ID, otherwise the spot was flagged and removed. Sequence files for both Affymetrix Drosophila array platforms (versions 1 and 2) were downloaded from the Affymetrix website . They contain a unique sequence for each probe set, which is searched (BLASTn; E-value < 10-6) against the genome to test for potential cross-hybridization. A segment of DNA associated with a probe set was assigned a v5.3 FlyBase gene ID.
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