genesbytimeseriesfoldchangebradyfl: Identify genes induced under bradyzoite conditions (CO2...

In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description

The goal of this experiment was to observe substantial transcriptional changes in <i>T. gondii</i> during tachyzoite-to-bradyzoite differentiation. Analysis of the two studied strains suggests that transcriptional changes associated with bradyzoite differentiation occur early after induction (within hours). <br><br> Human foreskin fibroblast (HFF) cells grown in D10 media within T25 flasks were inoculated with roughly 10,000 <i>T. gondii</i> parasites for each experiment. Two strains of <i>T. gondii</i> parasites were used in this analysis: type II Prugniaud lacking HXGPRT, and type III VEG. CO₂ starvation (MEM with 10% FBS, 25mM HEPES, pH 7.2 grown without CO₂) was used to induce in vitro bradyzoite differentiation.

Arguments

ts_fc_profile_two_fl	Choose a bradyzoite time series
ts_fc_two_fl	Choose one or more time point. NOTE: if more than one is chosen the fold change will be calculated using the average of all samples within the group Provide one or more values. Use comma as a delimter.
ts_fc_one_fl	Choose one or more time point. NOTE: if more than one is chosen the fold change will be calculated using the average of all samples within the group Provide one or more values. Use comma as a delimter.
fold_change	Enter a non-negative number. NOTE: Fold change is reported in the summary as positive numbers for up-regulated genes and negative numbers for down-regulated genes
regulated_dir	For ConditionA vs. ConditionB, select up-regulated for genes where ConditionA > ConditionB and select down-regulated for genes where ConditionB > ConditionA.
o-fields	Single valued attributes of the feature. Provide one or more values. Use comma as a delimter.
o-tables	Multi-valued attributes of the feature. Provide one or more values. Use comma as a delimter.
.convert	a logical value or a function that controls how the result of the method is returned. If this is a function, the character string or raw vector is passed to this function and it converts it appropriately. If this is a logical value and TRUE, then we attempt to convert the result based on its Content-Type returned by the Web server. If this is FALSE, the value from the Web server is returned as is.
.url	the URL for the Web request. This defaults to the correct value, but can be specified by the caller if the method is available at a different URL, e.g. locally or in a mirror server.
.json	a logical value controlling whether to use the JSON or the XML version of the method

Value

text/xml text/plain

duncantl/REuPathDB documentation built on May 15, 2019, 5:28 p.m.