Gene Validation

From AAAWiki

Contents 1 Overview 2 Array design and remapping 3 Expression results 4 Credits

Overview

This is expression data from microarray experiments to assay gene expression in each of six Drosophila species: Drosophila simulans, D. yakuba, D. ananassae, D. mojavensis, D. pseudoobscura, and D. virilis.

Array design and remapping

These are single-slide expression arrays - 380K spot slides from Nimblegen. Arrays are described in detail here

Probes were re-mapped to these annotation versions: CDS (Coding sequence from GLEANR consensus set. Downloaded from here on Nov. 21, 2006
Assembly: CAF1 with GenBank Coordinates, Oct. 30 2006 freeze downloaded from here on Nov. 17, 2006

Species	Total probes	# GLEANR probes	% GLEANR probes	# GLEANR probes	% GLEANR probes	# probes CAF1	% probes CAF1	# GLEAN nonCAF probes	% GLEAN nonCAF probes
D.sim	186,701	113,557	61	11,945	70	119,960	64	13,565	7
D.yak	190,097	136,367	72	13,889	71	146,538	77	17,051	9
D.ana	173,102	124,732	72	14,209	63	128,306	74	15,508	9
D.pse	190,109	163,407	86	12,471	72	159,829	84	19,575	10
D.moj	190,904	146,838	77	12,181	69	154,079	81	14,856	8
D.vir	187,293	149,943	80	12,440	70	150,393	80	15,936	9

Expression results

The table below summarizes expression analysis results from our arrays. Probe-level validation was performed on all probes that map to CAF1 Gene-level validation was performed using all probes that map to CAF1 AND to GLEANR annotation

Percentages of probes/genes refer to percent of probes/genes that remap to our array.

Validation results (from expression results v. 3.0)

Species	# probes yielding positive intensity	% of probes that remap	# genes with positive expression	% of genes that remap
D.sim	110859	92.41%	10634	82.19%
D.yak	123668	89.70%	12072	82.62%
D.ana	104778	87.82%	11378	77.45%
D.pse	148295	92.78%	11845	93.24%
D.moj	139302	90.41%	11018	88.30%
D.vir	135045	89.79%	11325	89.44%

Expression results v. 3.0
Nov 29, 2006

Species	Probes	Expr.Data
D.sim	fasta	gff
D.yak	fasta	gff
D.ana	fasta	gff
D.pse	fasta	gff
D.moj	fasta	gff
D.vir	fasta	gff

Each GFF file contains three tracks:
OLIV-PROBE: Coordinates only for all probes mapping perfectly to CAF1
OLIV-EXPR1: Coordinates for validated genes. Genes were validated by comparing signal intensity in probesets targeting each gene to the complete set of negative control probes (See array design description). Genes were called validated if they were significantly greater than negative controls at p < 0.001 by Mann-Whitney test, with p-values corrected by Benjamini and Hochberg. Score presented is the -log10. Only genes that passed the cutoff are in the track.
OLIV-EXPR2: Coordinates for probes yielding signal above background. Probes were considered above background if their mean intensity percentile rank were greater than the mean percentile rank of negative control probes. Score presented is mean percentile rank in either adult male or adult female (The higher of the two is presented). Only probes that passed the cutoff are in the track.

Credits

Updated Nov. 29, 2006

Dave Sturgill, Yu Zhang, Michael Parisi, and Brian Oliver at the Laboratory of Cellular and Developmental Biology, NIDDK, NIH. These results are unpublished. Please contact us at davidsturgill[AT]niddk.nih.gov if you are interested in using these data.