SCEPTRANS - Saccharomyces Cerevisiae  Periodic Transcription Server
Online Manual

Quick Start

Display a profile of one gene

  1. Type the systematic or common gene identifier, e.g. RNR1, or YNL300W into the GENE NAMES window.
  2. Hit the [!] (REPLACE) button just below the input area.
  3. Note that the gene identifiers are not case sensitive.
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Display profiles of two or more genes

  1. Type several gene identifiers separated by spaces or commas, e.g. RNR1, YNL300W,egt2 YBR160W into the GENE NAMES window.
  2. Hit the [!] (REPLACE) button just below the input area.
  3. The CLEAR button [X] will remove all text from the input field to let you start over easily.
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Add more genes to existing plots

  1. Type one or more gene identifiers into the GENE NAMES window.
  2. Hit the ADD [+] button below the input area.
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Remove one or more genes from your analysis

  1. Click on the gene id buttons in the GENE BUTTONS panel. The genes will appear in the GENE NAMES window.
  2. Hit the DELETE [-] button just below the GENE NAMES input area.
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Select experiment(s) from which to display data.

  1. Add or remove datasets from the display by clicking buttons in the TOGGLE DATASETS panel.
  2. In most browsers, active datasets will be highlighted in yellow.
  3. With no datasets selected, the default (YMC) will be activated.
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Select data analysis tools.

Three main tools for gene analysis are available:
  1. Gene features table
  2. Plots of temporal profiles or periodicity statistics
  3. Correlation matrices
Each of these can be switched on or off by the user by clicking the tool's SHOW [+] or HIDE [-] button. 		IMAGE

Advanced gene selection

Overview

The set of genes displayed in the analysis panel may be defined and modified by the user with a number of available selection tools. At each stage, a new set is defined, which may be merged with, substracted from, intersected with, or may replace the present set. The gene selection tools provide access to set operators in a manner similar to the Reverse Polish Notation: "define a selected set and then apply an operator acting on the old and selected sets". The set operators are accessible to the user as the following buttons:

[+] ADD
The new set will be the union of the previous and selected sets. It will contain all currently displayed genes and all newly selected ones.

[-] REMOVE
The new set will be the asymmetric difference of the previous and selected sets. It will contain the currently displayed genes excluding newly selected ones.

[!] REPLACE
The new set will consist of the selected genes. The current set will be forgotten.

[*] FILTER
The new set will be the intersection of the previous and selected sets. It will contain only those genes that are present both in the currently displayed and the newly selected set.

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Tools

 Restore previous set

The previous set of genes can be restored by clicking the [BACK] button in the gene selection panel.
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 Gene names

Gene identifiers (common or systematic) can be typed into the text box. Identifiers are case-insensitive, they should be separated by spaces or commas. Identifiers will be added automatically when clicked in the GENE BUTTONS panel.
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 Regular Expression search

This tool defines sets of genes by applying regular expression search to gene names, or gene descriptions in the SGD.
Examples:
  • Search gene names for tkl[0-9] for two variants of transketolase.
  • Search gene descriptions for mitochondri.*ribosom for mitochondrial ribosome subunit proteins.
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 Correlated profiles

Search for coexpressed genes. Coexpression is defined by high Pearson correlation coefficient of profiles in the linear scale.
  1. Select a profile to search around by providing a gene identifier (type or click in the GENE BUTTONS panel). Alternatively, click the [AVERAGE] button below to search around the average profile of currently displayed genes (in this case all must be expressed in the selected experiment).
  2. From the pull-down menu, select desired number of most closely coexpressed genes, or correlation coefficient threshold.
  3. Select dataset to compute correlations.
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 Peak to trough ratio

Define a set of genes based on peak to trough ratio in a given experiment.
  1. Select max/min expression ratio threshold.
  2. Select dataset in which to compute max/min expression ratio.
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 Periodic signal

Transcripts with significant periodicity measured by a single Fourier mode.
  1. Select dataset.
  2. Specify period corresponding to the queried Fourier mode. Default period lengths are provided for all datasets, but can be changed by the user.
  3. Select desired confidence level, defined as in Horne and Baliunas, Astrophysical Journal 302, 757, 1984.
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 Cellular localization

Genes whose products are localized to specified organelles within the cells, according to  Huh et al, Nature 425, 737, 2003.
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 Classified as regulated by different studies

Genes annotated as transcriptionally regulated by one of the following studies:
  • Tu et al., Science, 2005
  • Cho et al., Mol. Cell, 1998
  • Spellman et al., Mol. Biol. Cell, 1998
  • Pramila et al., Genes Dev., 2006
  • Rowicka et al., 2007 (in preparation)
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 MIPS functional categories

Genes in selected functional categories (first or second level) acording to MIPS. Holding down the [ctrl] key allows to select more than one category at a time.
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 Random genes

Adding genes selected by chance is sometimes useful to view the properties of a studied gene or a group of genes in the context of typical transcripts. The number of radom genes is selectable from a pull-down menu. Only the ADD and REPLACE operators are available with this selection.
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Analysis tools

Gene features table

This table presents summarized information about genes in the current set. Columns in the table contain respectively:
  • Common gene identifier (clickable; selects gene in gene selection tools).
  • Systematic gene identifier (clickable; selects gene in gene selection tools).
  • Cellular localization data.
  • MIPS functional annotation (switchable between description and numeric symbols).
  • Description according to SGD.
  • Peak to trough transcription ratios in selected experiments.
  • Transcriptional regulation reported by:
    • T Tu et al., Science, 2005
    • C Cho et al., Mol. Cell, 1998
    • S Spellman et al., Mol. Biol. Cell, 1998
    • P Pramila et al., Genes Dev., 2006
    • R Rowicka et al., 2007 in preparation, (high confidence set)
    • X Rowicka et al., 2007 in preparation, (extended set)
  • Link to the gene's page in SGD

Transcript plots

  • Plots of transcript concentration or periodicity statistics may be displayed by the Sceptrans server. The TIMESERIES plot (default) depicts concentration of mRNA as function of time. The user may choose to normalize the data to unit average, or to unit maximum from the SCALE TO menu.
  • Alternatively, one of three quantities measuring periodicity in the data may be displayed:
    • Autocorrelation.
    • Periodogram.
    • Periodogram significance.
    In these cases, the statistics ae plotted as functions of the period. The default period for a dataset is marked by a vertical line.
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Correlation tables

Tables of Pearson correlation coefficients of transcript profiles may be displayed for the selected genes. The entries are color-coded for easier interpretation. The user may also sort the selected genes by expression profile, which more clearly shows clusters of coexpressed genes.
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Examples

Correlation table of genes involved in DNA replication. Correlations within data from the alpha-30 experiment are shown, sorted by gene name (left), and by the alpha-30 expression profile (right).

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SCEPTRANS is optimized for firefox cite YEAST.SWMED.EDU Otwinowski Lab Department of Biochemistry UT SOUTHWESTERN
2005-2007 Andrzej Kudlicki
andrzej@work.swmed.edu