genesbypromastigotetimeseries: Find L.infantum genes based on expression differences...
In duncantl/REuPathDB: Interface to REST API of (EuPathDB)

Description Arguments Value

Find L. infantum genes based on expression differences in a L. donovani promastigote-to-amastigote differentiation time series. Axenic promastigote-to-amastigote differentiation of Leishmania donovani was induced by inoculating late-log phase promastigotes in medium 199 at pH 5.5 containing 25% fetal bovine serum and incubating them at 37C in 5% CO2 environment. RNA (and protein) was extracted from the cultures at 0 (promastigotes), 2.5, 5.0, 7.5, 10, 15, 24 and 144 (mature amastigotes) hr after exposure to the differentiation signal. cDNA was prepared by reverse transcription using random primers, labeled according to Nimblegen's standard protocol, and hybridized to a Nimblegen array based on the L. infantum v 3.0 sequence, supplemented by L. major sequence for some genes. Each protein-coding gene was represented by eight probes and placed on the microarray chip in triplicate. A total of 16 hybridizations were performed, one for each time-point in two biological replicates of this experiment. The raw data were subjected to quantile normalization across all chips, and a single value for each probe determined using a Tukey Biweight median value of the triplicates on each chip. A single CDS-level value for each chip was similarly determined by a Tukey Biweight median of all probes that map to a given gene. The gene-level signals were then log2-scaled to the corresponding 0 hour (promastigote) signal. This work was carried out by Tami Lahav, Neta Holland, Hanna Volpin & Dan Zilberstein at the Technion Institute, Israel and Amanda Anderson- Green, Dhileep Sivam and Peter Myler at Seattle Biomedical Research Institute, USA and is described in further detail in Sivam et al. (manuscript in preparation).

`ld_fc_profile_two_fl`	Choose a promastigote time series
`ld_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.
`ld_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.
`protein_coding_only`	Should only protein coding genes be returned?
`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