|
Transcript Name:
|
Generic name for the identified transcript.
|
|
Strand:
|
Denotes the direction of the transcripts. W transcript is present on the clockwise strand; C transcript is present on the counterclockwise strand.
|
|
Ig Size:
|
Total size of the intergenic region (in nucleotides). This is the number of nucleotides between the start/stop codons of the flanking ORFs.
|
|
From/To:
|
This denotes the location of the transcript with respect to the published E. coli genome sequence.
|
|
Size:
|
The size of the expressed transcript in nucleotides.
|
|
Left/Right Gene:
|
Indicates the name of the gene immediately to the left (the gene with the largest genomic coordinates less than the Ig region) or right (the gene with the smallest genomic coordinates greater than the Ig region) of the intergenic region.
|
|
Experiments:
|
Indicates the experimental conditions in which the transcript showed expression (Table 1).
|
|
Expression:
|
The maximum expression level of the transcript in any experiment (for each experiment, the average probe intensity of the transcript is calculated, and the number reported here is the maximum of these averages).
|
|
Cluster:
|
MAS 4.0 (Affymetrix, Santa Clara, CA) was used to cluster the expression profiles of Ig regions and ORFs via the self-organizing map (SOM) algorithm:
- Operon - All three expression profiles (the Ig transcript and its 2 flanking genes) are in the same cluster.
- 5UTR - Expression profiles of the downstream gene and the Ig transcript are in the same cluster.
- 3UTR - Expression profiles of the upstream gene and the Ig transcript are in the same cluster.
- Gene - The expression profiles of both genes which flank the Ig transcript are in the same cluster.
|
|
Homology:
|
Indicates all transcripts that have a p-value of < 0.01 and an overall identify to the Salmonella typhi sequence of > 65%.
|
|
E-value:
|
The E-value for the sequence homology analysis with Salmonella typhi (31).
|
|
Identity:
|
The percent sequence identity to Salmonella typhi.
|
|
Information:
|
Provides information on the identified transcript:
- (sRNA) - The name of previously identified sRNA transcripts (3-5).
- small RNA - Predicted small RNA.
- ORF (# nt) - Indicates that we predict a small ORF whose length is the given # of nucleotides, based on the Glimmer software (14).
- (colibri) - Predicted genes from the Colibri database (39).
- Operon candidate - Predicted operon element.
- P - Predicted operon from RegulonDB (33).
- D - Documented operon as listed in RegulonDB (33).
- Reg - Regulatory regions identified in RegulonDB (33).
- RT-PCR - Prediction verified through RT-PCR.
|