Input and runtime details for job 3236723 (precomputed example)

Input

	List of genes analyzed		YAP1 WWTR1 TP73 TEAD1 TEAD2 AJUBA BMP2 BMP4 BMP7 BMPR1A BMPR2 MYC NOG SMAD1 SMAD2 SMAD3 SMAD4 TGFB1 TGFB2 TGFB3 TGFBR1 TGFBR2 TGFBR3 -NF1 -NF2 -PTEN -TP53 -CHD5 -FOXD3
	Minimum number of genes per cluster		5
	Maximum number of genes per cluster		15
	Minimum score to return		1.1

Job ID 3236723 (server version 4.3.0)

	Job Submitted & Queued		@ Wed Aug 10 06:55:28 CEST 2016
	metaMIR Started		@ Wed Aug 10 06:55:39 CEST 2016
	metaMIR Finished & Post-Processing		@ Wed Aug 10 06:57:23 CEST 2016
	Job Completed		@ Wed Aug 10 06:57:23 CEST 2016

DIRECT ACCESS: http://rna.informatik.uni-freiburg.de/RetrieveResults.jsp?jobID=3236723&toolName=metaMIR ( 30 days expiry )

Description of the job

Combined differential and core analysis

As described, the Hippo/YAP pathway is involved in regulation of cell proliferation (specifically at the transcriptional co-activation, or nuclear component end) and the TGFb signalling pathway can be dysregulated (by overactivity) in many cancers (see example descriptions for core and differential analyses above). It is thus feasible that miRNAs may exist that simultaneously target members of both of these pathways, as both may encourage normal or pathological cell proliferation.

This gene list is a combination of the core and differential analyses. The core is set to the YAP-related members of the Hippo/YAP signalling pathway (marked with asterisks), the TGFb genes are as previously (to be targeted in any combination; any, all or none may be returned in the final list), and in a hypothetical therapeutic context, any returned miRNA is not to target tumour suppressors (prefixed with minus signs).

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_3236723//input_genes 5 15 1.1 /scratch/rna/bisge001/RNA_results/CARNA-result//metaMIR_3236723/" [1] "All entered genes ok." [1] "Partitioning positive genelist" [1] "Partitioning negative genelist" [1] "Analyzing 10 lists from 23 pos genes entered." | | | 0% | |======= | 10% | |============== | 20% | |===================== | 30% | |============================ | 40% | |=================================== | 50% | |========================================== | 60% | |================================================= | 70% | |======================================================== | 80% | |=============================================================== | 90% | |======================================================================| 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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