Research
Patterns of sequence conservation in presynaptic neural genes
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* Corresponding author: Maja Bućan bucan@pobox.upenn.edu
1 Penn Center for Bioinformatics, 423 Guardian Drive, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
2 Genomics and Computational Biology Graduate Group, 423 Guardian Drive, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
3 Department of Genetics in the School of Medicine, University of Pennsylvania, 415 Curie Boulevard Philadelphia, Pennsylvania 19104, USA
4 UCLA Neuroscience Graduate Office, 695 Young Drive South, Los Angeles, California 90095, USA
5 Department of Computer & Information Sciences in School of Engineering and Applied Sciences, 3330 Walnut Street, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
6 Department of Biology in the School of Arts and Sciences, 433 S University Avenue, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
Genome Biology 2006, 7:R105 doi:10.1186/gb-2006-7-11-r105
Published: 10 November 2006Additional files
Additional data file 1:
Overview of genomic regions of interest (gROIs)
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Additional data file 2:
VAMP phylogeny
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Additional data file 3:
RAB phylogeny
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Additional data file 4:
STX phylogeny
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Additional data file 5:
SYT phylogeny
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Additional data file 6:
RAB tree with superimposed expression profiles
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Additional data file 7:
Distribution of most conserved element (MCE) lengths
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Additional data file 8:
Palindromes found within most conserved element (MCE) subsequences
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Additional data file 9:
Differential expression of genes
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Additional data file 10:
The spreadsheet contains two worksheets. The 'chisq' worksheet lists transcription factor binding sites (TFBSs) differentially associated with the five expression clusters of presynaptic genes in decreasing order of statistical significance. The worksheet lists the TFBSs, the counts of occurrence of the TFBS in clusters 1 to 5, the expected number of TFBSs in clusters 1 to 5, the nominal c2 P value of observing such TFBS frequencies, and the Bonferroni-corrected P value. The 'z score' worksheet lists the TFBSs associated with a given expression profile in order of decreasing enrichment. The table lists the expression cluster number (1 to 5), the count of TFBSs across all clusters, the input size (base pairs) of genome queried for TFBS hits in the given cluster, the expected number of TFBS hits in the given cluster, enrichment, the natural log of the enrichment (the log likelihood), the z score, the P value associated with seeing up to the observed number of TFBSs in the given cluster, and the P value associated with seeing at least the observed TFBS in the given cluster (1 - P value).
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Additional data file 11:
Large most conserved elements (LMCEs) identified
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