Find genes based on expression differences between <i>L. infantum</i> promastigotes, intracellular amastigotes and axenic amastigote.<br><br> In this study, DNA oligonucleotide full-genome arrays representing all <i>L. infantum</i> annotated genes were used to determine global RNA expression profiling of axenic amastigotes and to assess how it compares to intracellular amastigotes. The full-genome DNA microarrays included one 70-oligonucleotides probe for each gene of <i>L. infantum</i>.<br> Intracellular amastigote analysis was a two-condition experiment, comparing promastigote stage to intracellular amastigote stage. This included six biological replicates for each stage, independently grown and harvested. One replicate per array. Axenic amastigote analysis was a two-condition experiment, comparing promastigote stage to axenic amastigote stage. This included four biological replicates for each stage, independently grown and harvested. One replicate per array.<br><br> Promastigote cells were grown in SDM-79 medium supplemented with 10% heat-inactivated fetal bovine serum and 5 micrograms/ml hemin at 25'C.<br>For intercellular amastigotes, amastigote cells were grown in THP-1 macrophage in RMPI 1640 medium supplemented with 10% heat-inactivated fetal bovine.<br>For axenic amastigotes, amastigote cells were isolated from infected mice or were grown in MAA20 medium supplemented with 20% heat-inactivated fetal bovine serum and 15 micrograms/ml hemin at 37'C.<br><br> For further details please refer: <a href="http://www.ncbi.nlm.nih.gov/pubmed/19393160">Whole-genome comparative RNA expression profiling of axenic and intracellular amastigote forms of <i>Leishmania infantum</i></a>
PaGE_comparisons_Li |
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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. |
confidence |
PaGE reports 1 - False Discovery Rate (FDR), which is called the "confidence" for the predictions. The FDR of a set of predictions is the expected percent of false predictions in the set of predictions. For example if the algorithm returns 100 genes with a false discovery rate of .3 (confidence=0.7) then we should expect 70 of them to be correct. |
protein_coding_only |
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o-fields |
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o-tables |
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.json |
a logical value controlling whether to use the JSON or the XML version of the method |
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