Computational protocol: Disruptions in a cluster of computationally identified enhancers near FOXC1 and GMDS may influence brain development

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Protocol publication

[…] Genome-wide locations of predicted transcription factor binding sites were generated using the Find Individual Motif Occurrences (FIMO) tool from the MEME suite of bioinformatics tools [], based on the April 2011 release TRANSFAC database of experimentally derived transcription factor binding motifs [], with a FIMO score threshold of 10e−5. We intersected these predicted binding sites with the genomic coordinates of the four enhancers using the IntersectBed tool from the BedTools suite of bioinformatics tools [].To determine which genes were expressed in the developing brain, we used the fetal brain data from the GNF Atlas2 database []. The fetal brain data included in GNF Atlas2 is based on a Clontech pooled sample of normal whole brains from 59 spontaneously aborted male and female Caucasian fetuses, ages 20–33 weeks. All array data was mapped to RefSeq gene names (RefGene track downloaded from the UCSC Genome Browser January 2014). Genes with an expression score greater than or equal to 64 were considered expressed. To assess known gene expression patterns in the developing mouse, we viewed images of in situ hybridizations of E11.5 and E14.5 mouse embryos from the Allen Brain Map (http://developingmouse.brain-map.org/) and the Eurexpress Transcriptome Atlas (http://www.eurexpress.org/ee/). To assess known gene expression in the developing human brain, we viewed RNA-seq data from the BrainSpan Atlas of the Developing Human Brain (http://www.brainspan.org/). Genes with RPKM (reads per kilobase per million) values greater than 1 were considered to be expressed []. […]

Pipeline specifications

Software tools MEME Suite, BEDTools, Atlas2
Databases Eurexpress RefGene BrainSpan UCSC Genome Browser
Applications RNA-seq analysis, Genome data visualization
Organisms Homo sapiens
Chemicals Mannose