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 complete results [zip]

Result table

Sort by selecting a column name.

miRNA	Final Score	Positive Combo	Positive Score	Positive Group	Positive List
hsa-miR-6508-5p	2.218	SMAD2,SMAD3,TEAD1,TGFBR3,TP73,YAP1	2.067	6	1.9
hsa-miR-5681a	1.813	BMPR2,SMAD1,SMAD3,TEAD1,TGFBR3,WWTR1,YAP1	1.462	7	1.81
hsa-miR-548az-5p	1.222	AJUBA,BMPR2,SMAD1,SMAD4,TEAD1,TGFBR3	1.197	6	1.21
hsa-miR-4695-5p	2.307	BMP2,BMPR2,SMAD1,SMAD3,SMAD4,TEAD1,WWTR1	1.17	7	2.31

Result table - repPos

Sort by selecting a column name.

Gene name	Rep
BMPR1A	100
BMPR2	100
SMAD2	100
SMAD3	100
SMAD4	100
TEAD1	100
TGFBR1	100
TGFBR2	100
TGFBR3	100
WWTR1	100
TGFB2	90
AJUBA	80
BMP2	80
YAP1	80
TP73	60
BMP7	40
BMP4	10
MYC	10
NOG	10
SMAD1	10
TEAD2	10
TGFB1	10
TGFB3	10

Result table - clusterPos

Show rows: 1-10 11-20 21-30 31-37 all

Sort by selecting a column name.

Gene 1	Inter	Gene 2	Norm
AJUBA	pp	BMP2	19
BMPR1A	pp	BMPR2	23
SMAD2	pp	SMAD3	23
SMAD4	pp	TEAD1	23
TGFB2	pp	TGFBR1	20
TGFBR2	pp	TGFBR3	23
TP73	pp	WWTR1	18
YAP1	pp	AJUBA	19
BMP2	pp	BMPR1A	15
BMPR2	pp	SMAD2	20

Rows: 1-10 11-20 21-30 31-37 all

Job resubmission

Use the following button if you want to resubmit the job with altered input or parameterization:

usability assessment

Please support us by filling this short quality survey for evaluating this

service.

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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Input and runtime details for job 3236723 (precomputed example)

Input

Job ID 3236723 (server version 4.3.0)

Description of the job

Output download complete results [zip]

Result table

Result table - repPos

Result table - clusterPos

Job resubmission

usability assessment

When using metaMIR please cite :