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ConTra allows its user to select only single values from each attribute before mining the dataset for the existence of such contradictions.
ConTra identifies contradictions by allowing its users to select two or more values from an investigated attribute before mining the dataset for the existence of such contradicting attribute values in a particular object.
We believe that by utilizing a combination of approaches including mining the dataset of transcriptionally altered genes that are specifically related to the pathogenesis of ECM and further investigations in gene knockout mice and immunohistology studies, we have identified three novel host molecules – CD14, galectin-3 and OX40 that may play a critical role in the pathogenesis of ECM.
Mining the dataset with other analytical approaches might lead to a different set of potential biomarkers.
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In order to better understand the mechanisms employed by the NR family, gene expression data were used i) for the 48 human NR genes (provided by AstraZeneca) and ii) for the 49 mouse NR genes, by mining the published dataset of Bookout et al [ 2].
After the analysis of c-Myc targets (Chen et al, 2008) by mining the RNA-seq dataset, we found that 95 out of the 2,449 Smg6 DEGs were regulated by c-Myc (Supplementary Tables S4 and S5).
Then they mined the cMap dataset to identify drugs that had SDEs that opposed those of IBD.
To identify putative TM proteins from the planarian transcriptome, we mined the 454 dataset for putative TM protein-encoding messages (see Methods).
ConTra graphically represents contradictory data from a noisy dataset by mining the contradictory data in the investigated dataset and enabling the visualisation of such data in a pie chart.
We mined the entire datasets of predicted proteins from eight animal species (see Figure 1) as well as two unicellular species of yeast for SLC17 proteins using a sequence Hidden Markov Model (HMM) trained on the alignment containing the nine human SLC17 protein sequences.
By mining the data from several validation datasets it was possible to determine which factors contribute to the variance in normalized DNA-microarray data.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com