Input and runtime details for job 5275471 (precomputed example)
Input
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 |
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 complete results [zip]
Result table
miRNA | Final Score | Positive Combo | Positive Score | Positive Group | Positive List |
---|---|---|---|---|---|
hsa-miR-8064 | 2.07 | AJUBA,FOXI1,PAX3,TEAD1,TP73 | 2.143 | 5 | L04 |
hsa-miR-6865-3p | 2.12 | AJUBA,PAX3,PAX7,SMAD4,YAP1 | 2.117 | 5 | L01 |
hsa-miR-376a-2-5p | 2.11 | AJUBA,MSX1,SMAD4,TEAD1,YAP1 | 2.112 | 5 | L07 |
hsa-miR-1268b | 2.05 | GBX2,MSX1,MSX2,TP73,WWTR1 | 2.046 | 5 | L07 |
hsa-miR-4707-5p | 1.84 | MSX2,SMAD4,TEAD1,TP73,ZIC5 | 1.896 | 5 | L09 |
hsa-miR-208b-5p | 1.88 | AJUBA,FOXI1,SMAD2,TEAD1,ZIC1 | 1.893 | 5 | L04 |
hsa-miR-548ba | 1.88 | DLX6,SMAD2,SMAD3,TEAD1,YAP1 | 1.883 | 5 | L03 |
hsa-miR-624-5p | 1.83 | PAX3,SMAD2,SMAD3,WWTR1,YAP1 | 1.831 | 5 | L01 |
hsa-miR-8067 | 1.74 | AJUBA,FOXI1,SMAD4,TP73,WWTR1 | 1.741 | 5 | L04 |
hsa-miR-424-3p | 1.64 | HES5,SMAD3,SMAD4,WWTR1,YAP1 | 1.701 | 5 | L06 |
Result table - repPos
Gene name | Rep |
---|---|
AJUBA | 100 |
GBX2 | 100 |
MSX2 | 100 |
PAX3 | 100 |
PAX7 | 100 |
SMAD2 | 100 |
SMAD3 | 100 |
SMAD4 | 100 |
TEAD1 | 100 |
TFAP2A | 100 |
Result table - clusterPos
Gene 1 | Inter | Gene 2 | Norm |
---|---|---|---|
AJUBA | pp | GBX2 | 19 |
MSX2 | pp | MYC | 15 |
PAX3 | pp | PAX7 | 23 |
SMAD2 | pp | SMAD3 | 23 |
SMAD4 | pp | TEAD1 | 23 |
TFAP2A | pp | TP73 | 21 |
WWTR1 | pp | YAP1 | 23 |
ZIC1 | pp | AJUBA | 21 |
GBX2 | pp | MSX2 | 20 |
MYC | pp | PAX3 | 15 |
Job resubmission
usability assessment
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.