For each oligonucleotide that showed multiple hits, the corresponding gene identifiers of all found hits were given in the description line in order not to lose potentially important information.
We present AmalgamScope a new interactive software tool focusing on assisting scientists with the annotation of the human genome and particularly the integration of the annotation files from multiple data types, using gene identifiers and genomic coordinates.
The paper " AmalgamScope: merging annotations data across the human genome" presents a new interactive software tool developed to assist scientists with annotation of the human genome and in particular the integration of the annotations from multiple data types, using gene identifiers and genomic coordinates.
The Gene column consists of gene identifiers while the Gene name identifies the name of each of the gene identifier.
Gene names were mapped to Ensembl gene identifiers [ 24].
As a summary statistic for multiple probesets that match to the same entrez gene identifiers we used the median expression value.
For counting significant differentially expressed genes, probe set identifiers were mapped to Entrez Gene identifiers.
Sample data tables index expression measurements of multiple RNA transcripts with Probe Set IDs, while the external gene identifiers, names, and symbols were stored in platform data tables.
For instance, while there is usually a one-to-one mapping from UniProtKB to Entrez Gene identifiers, mapping in the opposite direction may produce multiple results as one gene can be responsible for several protein variants or fragments.
Following the procedure of Su et al. (2001), for each tumor sample, raw intensity values were thresholded at 20. Mappings from the probe identifier to Ensembl gene identifiers were downloaded from the Affymetrix web site, and multiple probes matching the same Ensembl gene identifier were averaged together to produce a single measurement for each gene.
