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Supporting material for paper: A putative role for g...

Created: 2013-11-06 10:34:47 | Last updated: 2017-04-19 11:22:27

This pack contains links that refer to the myExperiment packs and Research object links that describe our two sets of workflow implementation, for data analysis and for data interpretation.

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Annotate gene list with top ranking concepts (4)

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This workflow annotates a comma separated gene list with a predefined concept set as for example Biological processes or Disease/syndrome. To obtain the particular id for each concept set (e.g. "5" for Biological processes), the workflow listPredefinedConceptSets needs to run first. The output provides us with the top (cutoff) concepts that describe our gene list of interest The workflow is using the anni web services .

Created: 2013-12-03 | Last updated: 2015-04-03

Credits: Eleni

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Supplementary file 5: Percentile scores

Created: 2016-10-25 15:05:47

Credits: Eleni

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document presents the percentile score of the prioritized gene list when compared to the frequency distribution of 100 match scores of randomly sampled gene-HTT concept pairs out of the 12,391 genes in our concept profile database.

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Supplementary file 4: Decision about the promoter re...

Created: 2016-10-25 15:05:15

Credits: Eleni

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This document is included as a reference to describe the decisions that were made concerning the promoter size using an older version of epigenetic data from ENCODE. In this file we present the additional runs of the workflow compute\_overlaps that were performed with different parameters in order to test and decide for the best promoter region and overlap parameters.

File type: Word document

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Supplementary file 3: Gene prioritization

Created: 2016-10-25 15:04:40

Credits: Eleni

License: Creative Commons Attribution-Share Alike 3.0 Unported License

Top 100 novel proteins, resulted from the semantic analysis associated with HTT and epigenetics

File type: Excel workbook

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Supplementary file 2: Annotations of CpG containing ...

Created: 2016-10-25 15:03:45

Credits: Eleni

License: Creative Commons Attribution-Share Alike 3.0 Unported License

The top 50 annotations characterising each group of genes with CpG islands and without, resulted from the semantic analysis of those two groups of genes with Biological Processes.

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Supplementary file 1: Unique annotations of genes in...

Created: 2016-10-25 15:01:52

Credits: Eleni

License: Creative Commons Attribution-Share Alike 3.0 Unported License

This file contains the results from the semantic analysis with Biological Processes of the genes that were overlapping with active TSS, bivalent TSS, heterochromatin and repressed polycomb chromatin state. The annotations that we present here are uniquely characterizing each gene list (as resulted from the CPA out of the top 50 annotations).

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Eleni

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Supplementary information for paper submission @ F10...

Created: 2016-10-25 14:57:58 | Last updated: 2016-10-25 15:06:18

This pack contains the files that belong to supplementary information of the paper submission at F1000Research. Note: This is a temporary link for the review proccess of the thesis "Knowledge discovery methods in Huntington's Disease" by Eleni Mina, till the data are published online at the F1000Research

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Create nanopublications (1)