Input and runtime details for job 5275471 (precomputed example)

Input

	List of genes analyzed		YAP1 WWTR1 TP73 TEAD1 TEAD2 AJUBA MYC PAX3 PAX7 DLX5 DLX6 FOXI1 GBX2 HES1 HES5 MSX1 MSX2 SMAD2 SMAD3 SMAD4 TFAP2A ZIC1 ZIC5
	Minimum number of genes per cluster		5
	Maximum number of genes per cluster		15
	Minimum score to return		1.1

Job ID 5275471 (server version 4.3.0)

	Job Submitted & Queued		@ Mon Aug 08 10:15:17 CEST 2016
	metaMIR Started		@ Mon Aug 08 10:15:24 CEST 2016
	metaMIR Finished & Post-Processing		@ Mon Aug 08 10:16:28 CEST 2016
	Job Completed		@ Mon Aug 08 10:16:28 CEST 2016

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=5275471&toolName=metaMIR ( 30 days expiry )

Description of the job

example2

An example investigating potential miRNA-mediated cross regulation between two cellular processes: the Hippo/YAP signaling pathway and transcription factors involved in neural crest (NC) development. Specifically, co-regulation here is investigated between those factors promoting Hippo/YAP transcriptional co-activity and transcription factors involved in the neural plate border specification during NC development.

The Hippo/YAP genes are marked with asterisks, to ensure that any combination returned in the analysis will have at least one YAP-related component subject to simultaneous co-regulation with NC genes. Otherwise, the results could be overwhelmed by the much longer list of NC genes, returning combinations that contain no Hippo/YAP elements.

Output

Download an archive file containing the complete results produced by the job in [.zip] format.

Results file content

[1] "input= /scratch/rna/bisge001/RNA_results/CARNA-result//metaMIR_5275471//input_genes 5 15 1.1 /scratch/rna/bisge001/RNA_results/CARNA-result//metaMIR_5275471/" [1] "All entered genes ok." [1] "Partitioning positive genelist" [1] "Analyzing 9 lists from 23 pos genes entered." | | | 0% | |======== | 11% | |================ | 22% | |======================= | 33% | |=============================== | 44% | |======================================= | 56% | |=============================================== | 67% | |====================================================== | 78% | |============================================================== | 89% | |======================================================================| 100%[1] "Assigning proportions of defined core" [1] "Writing results"

When using metaMIR please cite :

Jason A. Davis, Sita J. Saunders, Martin Mann, Rolf Backofen
Combinatorial ensemble miRNA target prediction of co-regulation networks with non-prediction data
Nucleic Acids Research, 2017, 45 (15), 8745–8757.
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46(W1), W25-W29, 2018.

Results are computed with metaMIR version 1.0.0 using R 3.2.1

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