SAGE tags

More than 300 transcripts, identified in treatment comparisons, had a five-fold or greater difference in abundance. The ten most abundant SAGE tags identified in the UV-treated SAGE library are listed in Table 11.1. Greater than... 

Table 11.1 The ten most abundant SAGE tags identified in the UV-treated SAGE library.

We mapped all SAGE tags to the genes they represented as follows. We used the standalone Blast from NCBI (ftp //ftp.ncbi.nlm.nih. 

Sequence data for SAGE tags allows profiling of gene expression. 

An experimental strategy was developed called screening poly(dA/dT) cDNAs for gene identification to overcome the above-described imbalances. Tire methodology experimentally increased the rate of novel gene identification in direct screening and SAGE tag collection. 

This tool extracts up to four possible SAGE tags and orientalion signals from a sequence. Orientation signals aMowlhs most likely tag to be chosen (sequences are usually written in the 5 -3 [+) or 3 -5 (-) orienlions),... 

Abbreviation Bp, nucleotide base pairs cDNA, complementary DNA ChIP, chromatin Immunoprecipi-tation Cy5, cyanine 5-dCTP Cy3, cyanine 3-dCTP ESTs, expressed sequence tags FDR, false discovery rate MIAME, minimum information about a microarray experiment mRNA, RNA, messenger NIA, National Institutes of Aging RFUs, relative fluorescence units RT-PCR, reverse transcriptase polymerase chain reaction SAGE, serial analysis of gene expression SAM, significance analysis of microarrays... 

SAGE [7] involves the concatenation of short nucleotide sequence tags (9-10 bp), each representative of a different gene. The concatenated tags are then cloned and sequenced. The prevalence of a particular tag corresponds to the abundance of the corresponding mRNA in the sample. 

There are direct measures of gene expression, but these tend to be limited by expense. They include TaqMan assays, which can measure the expression of several hundred genes directly, massively parallel signature sequencing (MPSS), expressed sequence tag (EST) counts, and serial analysis of gene expression (SAGE). Microarrays measure gene expression indirectly, and dye effects such as the dye bias of Cy3/Cy5 require lowess correction. 

CAGE is similar to SAGE in principle however, it is based on preparation and sequencing of concatamers of DNA tags deriving from the initial 20 nucleotides from 5 end mRNAs. 

Figure 16.1. Serial Analysis of Gene Expression (SAGE) depends on the generation of a tag from the 3 end of an mRNA, Tags are concatemerized and sequenced. These data are compared with a database of tags linked to individual transcriptsto generate the frequency of each tag in the library, a measure of the expression level for that gene. (See color plate.)...

Follow the tag hotlinks in the output table to find out its expression level in different SAGE libraries and how it is represented in the rest of the sequences in GenBank and UnlGene. 

Figure 16.6. The complete list of tags from the virtual Northern results (Figs. 16.4 and 16.5) can also be used to query the database, finding the occurrence of their tags in all SAGE libraries.

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