May 4th 2009 - README for gencode_exons_rpkm_4_exp.gff * gencode_exons_rpkm_4_exp.gff is a version2 gff file containing Gencode exons associated to expression values for 4 RNAseq experiments and 12 tiling array experiments * Each line represents a different distinct Gencode exon which is given a name corresponding to the Gencode gene it comes from and its order in this gene. The RNAseq expression values are RPKM values provided by Ali M., and the tiling array expression values are means of intensities of probes overlapping the exons. * Here is an example: chr1 genc ex 1873 1920 . . . name: RP11-34P13.1/1 k2x75: 0.63 k2x75r2: 0.00 g2x75: 0.00 g2x75r2: 0.00 tpgc 0 tpkc 0 tpkn 0 tppw 0 tmgc 0 tmgn 0 tmkc 0 tmkn 0 tmkp 0 tmpw 0 ttkh 0 ttku 0 * The information provided is the following: - field no 1: Gencode exon chromosome - field no 2: genc - field no 3: ex - field no 4: Gencode exon start coordinate - field no 5: Gencode exon end coordinate - field no 6: . - field no 7: . - field no 8: . - field no 9: list of (key,value): ** Gencode exon name according to nomenclature explained above (provided by Ali M.) ** RPKM value from paired end read RNAseq experiment of polyA+ K562 Whole cell replicate 1 (454, 2*75bp) ** RPKM value from paired end read RNAseq experiment of polyA+ K562 Whole cell replicate 2 (454, 2*75bp) ** RPKM value from paired end read RNAseq experiment of polyA+ GM12878 Whole cell replicate 1 (454, 2*75bp) ** RPKM value from paired end read RNAseq experiment of polyA+ GM12878 Whole cell replicate 2 (454, 2*75bp) ** Mean probe intensity from tiling array experiment of PolyA+ GM12878 cytosol ** Mean probe intensity from tiling array experiment of PolyA+ K562 cytosol ** Mean probe intensity from tiling array experiment of PolyA+ K562 nucleus ** Mean probe intensity from tiling array experiment of PolyA+ Prostate Whole cell ** Mean probe intensity from tiling array experiment of PolyA- GM12878 cytosol ** Mean probe intensity from tiling array experiment of PolyA- GM12878 nucleus ** Mean probe intensity from tiling array experiment of PolyA- K562 cytosol ** Mean probe intensity from tiling array experiment of PolyA- K562 nucleus ** Mean probe intensity from tiling array experiment of PolyA- K562 polysomes ** Mean probe intensity from tiling array experiment of PolyA- Prostate Whole cell ** Mean probe intensity from tiling array experiment of total K562 Chromatin ** Mean probe intensity from tiling array experiment of total K562 Nucleolus