plotGenomic

Created: 2013-10-07 15:02:26

Download Workflow

This workflow returns a graphical representation of selected Nencki Genomics Database (www.nencki-genomics.org) content in the ± 10 kb flank of the transcription start site of a chosen gene.

More precisely, it returns instances of selected area types, and instances of selected motif types that intersect any of the returned area instances. The results are returned as three files: a pdf file with the plot, and two tab-separated files with the details of areas and motifs shown in the plot.

Publication doi: 10.1093/database/bat069

Preview

Download as scalable diagram (SVG)

Run

Run this Workflow in the Taverna Workbench...

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://myexperiment.org/workflows/3850/download?version=1
[ More Info Expand ]

Workflow Components

Authors (1)

Titles (1)

Descriptions (1)

Dependencies (0)

Inputs (9)

Name	Description
species	NGD species short name. Choice of: hsap, mmus, rnor.
version	NGD version, usually the Ensembl version followed by "_1".
gene	Ensembl gene display_label, e.g. BDNF (Bdnf); or gene_stable_id, e.g. ENSG00000176697.
library	A motif library to use. Choice of: jaspar, transfac, genomatix. (The last accessible only to local registered users.)
motif_name	A list of motifs to be plotted, from Jaspar or Transfac Professional motif libraries. Motifs can be entered either as a list of dataset types e.g. (for Jaspar): MA0018.1, PB0108.1, PB0010.1; or as a list of transcription factor names, e.g. (for Jaspar): CREB1, Atf1_2, Egr1_1. Click 'Add value' to use the example transcription factor name (CREB1). Use 'Add value' to add additional motifs. Delete all elements from the input list, or replace the example value with xsi:nil to to plot only the areas.
area_types	A list of NGD area type(s) to be plotted. Click "Add value" and use the default null value (xsi:nil) to plot all the area types. Delete the default null value (xsi:nil), and then click 'Add value' to enter particular area types, e.g.: CREB, cisRED Search Region. Enter one type per list element.
separate_motifs	When this flag is set to 'True' , different motifs assigned to the same tf_name (e.g. the motifs MA0018.1 and MA0018.2 for the tf_name CREB1) are ploted in separate lines.
user	Authenticating user.
passwd	Authenticating user password. None (encoded as xsi:nil) for the user 'public'.

Processors (7)

Name	Type	Description
PlotGenomicResponse	xmlsplitter
PlotGenomicResponse_PlotGenomicResult	xmlsplitter
PlotGenomicResult_PlotGenomicResult	xmlsplitter
PlotGenomic	wsdl	Wsdl http://webservices.nencki-genomics.org/genomic?wsdl Wsdl Operation PlotGenomic
PlotGenomic_2	xmlsplitter
authenticate	xmlsplitter
input	xmlsplitter

Beanshells (0)

Outputs (2)

Name	Description
file_name
file_data

Datalinks (17)

Source	Sink
PlotGenomic:PlotGenomicResponse	PlotGenomicResponse:input
PlotGenomicResponse:PlotGenomicResult	PlotGenomicResponse_PlotGenomicResult:input
PlotGenomicResponse_PlotGenomicResult:PlotGenomicResult	PlotGenomicResult_PlotGenomicResult:input
PlotGenomic_2:output	PlotGenomic:PlotGenomic
authenticate:output	PlotGenomic_2:authenticate
input:output	PlotGenomic_2:parameters
passwd	authenticate:password
user	authenticate:username
species	authenticate:species
version	authenticate:version
area_types	input:area_types
gene	input:gene
library	input:library
motif_name	input:motif_name
separate_motifs	input:seperate_motifs
PlotGenomicResult_PlotGenomicResult:file_name	file_name
PlotGenomicResult_PlotGenomicResult:file_data	file_data

Coordinations (0)

Information Workflow Type

Taverna 2

Information Uploader

mdabr

Information License

All versions of this Workflow are licensed under:

Information Version 1 (of 1)

Information Credits (1)

(People/Groups)

mdabr

Information Attributions (0)

(Workflows/Files)

None

Information Tags (11)

Uploader tags

Log in to add Tags

Information Shared with Groups (0)

None

Information Featured In Packs (0)

None

Log in to add to one of your Packs

Information Attributed By (0)

(Workflows/Files)

None

Information Favourited By (0)

No one

Information Statistics

881 viewings

725 downloads

[ see breakdown ]

Citations (1)

1. Izabella Krystkowiak; Jakub Lenart; Konrad Debski; Piotr Kuterba; Michal Petas; Bozena Kaminska; Michal Dabrowski, Nencki Genomics Database--Ensembl funcgen enhanced with intersections, user data and genome-wide TFBS motifs, Database 2013; doi: 10.1093/database/bat069, 02 October 2013, http://database.oxfordjournals.org/cgi/content/full/bat069? ijkey=ml5GxAmJmA0S7wS&keytype=ref

Version History

In chronological order:

plotGenomic

Created by mdabr on Monday 07 October 2013 15:02:25 (UTC)

Reviews (0)

No reviews yet

Be the first to review!

Comments (0)

View Timeline

No comments yet

Log in to make a comment

Other workflows that use similar services (1)

Taverna 2

Uploader

mdabr

showDatasetsGenomic (1)

Download

Shows all the datasets available in the Nencki Genomics Database (www.nencki-genomics.org). Click 'Use examples' to see all the datasets, separated into datasets of TFBS motifs, and all the remaining datasets (areas), the latter including data from Ensembl funcgen and (thus) Encode. Publication doi: 10.1093/database/bat069

Created: 2013-10-07

Credits: mdabr

plotGenomic

Preview

Run

Run this Workflow in the Taverna Workbench...

Workflow Components

Wsdl

Wsdl Operation

Reviews (0)

Comments (0)

Other workflows that use similar services (1)