The supporting materials further comprise assembled panel of variability (folders P3.1, P3.2), alignment of expression parameters (including variability) with target mechanistic data (P3.3, P3.4), the files P4 supports ontological analysis.
SK contributed to the concept of alignment of expression profiles, invented and implemented primary methodology and primarily wrote the manuscript.
Data types IGB can display include gene structure annotations, shown as linked blocks with taller blocks indicating translated regions; genomic alignments of expression array target sequences and probes, shown as linked blocks bearing smaller blocks representing probes; and EST/cDNA genomic alignments, shown as linked spans.
Alignment of gene expression patterns with the phases described above (see Results section) in their spatial context may eventually help identify genes that are critical to bone regeneration but appear at low levels within the more dominant spatial domains at any particular time.
AGEP: alignment of gene expression profiles; CUP: cancer of unknown primary origin; GEO: Gene Expression Omnibus; GIST: gastrointestinal stromal tumor; LOOCV: leave-one-out cross-validation; tm-score: tissue match score; ts-score: tissue specificity score; wAGEP: weighted AGEP.
For this purpose, we analyzed test samples by aligning their microarray profiles against the annotated and normalized GeneSapiens microarray reference database and applied a slightly modified alignment of gene expression profiles (AGEP) method - weighted AGEP (wAGEP) - which we recently developed and described for classification of cell differentiation patterns [ 22].
Phylogenies can be inferred from many types of data, e.g. protein/DNA alignments, results of expression clustering and Interpro hierarchies, using specialist phylogenetics packages such as Phylip [1], Paup [2] and others.
HT conceived of the study, participated in sequence alignments and analyses of expression profiles and substantially drafted the manuscript.
Aach and Church implemented both simple and interpolative time warping based on dynamic programming to identify an optimal alignment of two gene expression time series [ 11].
Moreover, chronological alignment of UPR pathways' expression, shutdown, and ensuing cell death is in agreement with the mechanism of cell fate regulation allocated with the UPR (Lin et al, 2007).
We have created a rapid and powerful approach for the alignment of microarray gene expression profiles (AGEP) from test samples with those contained in a large annotated public reference database and demonstrate here how this can facilitate interpretation of microarray data from individual samples.
