Search for phylogenetically conserved promoter models

[Introduction] [Homology Group Selection] [Parameters] [Output]

Introduction

This task allows to search for transcription factor binding site models that are conserved in orthologous promoter sequences of several vertebrate species. This way further evidence for the functionality of promoter models can be gained because TF models are more likely to be functional when they have been preserved during evolution.

The Genomatix homology groups (defined by a proprietary algorithm, see Comparative Genomics) include 16 vertebrate species (Homo sapiens, Pan troglodytes, Macaca mulatta, Mus musculus, Oryctolagus cuniculus, Rattus norvegicus, Equus caballus, Canis lupus familiaris, Bos taurus, Sus scrofa, Monodelphis domestica, Ornithorhynchus anatinus, Xenopus tropicalis, Danio rerio, Gallus gallus, Taeniopygia guttata). A promoter model is defined to be conserved if it is found in at least one alternative promoter sequence of the genes in a homology group for all selected organisms.

Homology Group Selection

Homology Group Selection
Select organism	Select the organisms for which the orthologous promoter sequences should be analyzed. The homology groups always correspond to the latest ElDorado release. You can select all vertebrates or at least two individual organisms from the following list: Homo sapiens Macaca mulatta Pan troglodytes Mus musculus Oryctolagus cuniculus Rattus norvegicus Equus caballus Canis lupus familiaris Bos taurus Sus scrofa Monodelphis domestica Ornithorhynchus anatinus Xenopus tropicalis Danio rerio Gallus gallus Taeniopygia guttata
Constraints	You can set one or several mandatory organisms in which promoter model matchess have to be present. Please note that all mandatory organisms need to be included in the organisms selected for the search. The second constraint is the minimum number of organisms for which promoter model matches have to be found in the same homology group. The number has to be equal or lower than the number of organisms selected.

Select organism

Select the organisms for which the orthologous promoter sequences should be analyzed. The homology groups always correspond to the latest ElDorado release.

You can select all vertebrates or at least two individual organisms from the following list:

Homo sapiens
Macaca mulatta
Pan troglodytes
Mus musculus
Oryctolagus cuniculus
Rattus norvegicus
Equus caballus
Canis lupus familiaris
Bos taurus
Sus scrofa
Monodelphis domestica
Ornithorhynchus anatinus
Xenopus tropicalis
Danio rerio
Gallus gallus
Taeniopygia guttata

Constraints

You can set one or several mandatory organisms in which promoter model matchess have to be present. Please note that all mandatory organisms need to be included in the organisms selected for the search.

The second constraint is the minimum number of organisms for which promoter model matches have to be found in the same homology group. The number has to be equal or lower than the number of organisms selected.

Parameters

Parameters
Model groups	Please choose one or several of the available Genomatix model libraries. If you have created your own models with FastM or FrameWorker, they can be found in the "User-defined models"-library. You can decide if you want to use all the models in the chosen libraries use previously defined model subsets or continue with a subset selection. In the third case, there will be a separate page with a list of all models in the chosen libraries and you can select your model subset by clicking the checkboxes for each model.
Further parameters	All further parameters (e.g. "Max. number of matches") correspond to the ModelInspector search and output parameters.
Email address	Here you can choose between two methods for receiving the results: Show result directly in browser window In this option the URL of the result is directly shown in your browser window. Warning: Please use this option only for analyses which can be performed in a short time. If the analysis takes longer than the timeout of the webserver, the connection will be terminated and you will receive an error message (e.g. "The document contained no data."). In this case, the results will not be available, please restart the analysis using the option below "Send the URL of the result to". Send the URL of the result via email In this option an email with the URL of the results will be sent to the user provided email address, when the analysis is finished. The results will be available for a limited time on our server. For details of how long your results will be kept please see the result-email. After that period they will be deleted unless protected in the project management!

Model groups

Please choose one or several of the available Genomatix model libraries.
If you have created your own models with FastM or FrameWorker, they can be found in the "User-defined models"-library.

You can decide if you want to

use all the models in the chosen libraries
use previously defined model subsets or
continue with a subset selection.

In the third case, there will be a separate page with a list of all models in the chosen libraries and you can select your model subset by clicking the checkboxes for each model.

Further parameters

All further parameters (e.g. "Max. number of matches") correspond to the ModelInspector search and output parameters.

Email address

Here you can choose between two methods for receiving the results:

Show result directly in browser window
In this option the URL of the result is directly shown in your browser window.
Warning: Please use this option only for analyses which can be performed in a short time.
If the analysis takes longer than the timeout of the webserver, the connection will be terminated and you will receive an error message (e.g. "The document contained no data."). In this case, the results will not be available, please restart the analysis using the option below "Send the URL of the result to".
Send the URL of the result via email
In this option an email with the URL of the results will be sent to the user provided email address, when the analysis is finished.

The results will be available for a limited time on our server. For details of how long your results will be kept please see the result-email. After that period they will be deleted unless protected in the project management!

Output

Three output files are generated: the match overview, the detailed output, and the statistics file.

1. Match overview

The first output file contains:

The selected input parameters.

Example:

Sequence file:	Vertebrate homologous promoters
Selected organisms:	Homo sapiens, Mus musculus, Rattus norvegicus, Gallus gallus, Canis lupus familiaris, Bos taurus
Models:	Vertebrate_Modules/CEBP_HNF1_02.model
Strand(s) searched:	both strands
Threshold for number of elements:	100.0 % (2 of 2 elements)
Output sorted by:	match positions on the sequences
Matches have to occur in:	orthologous promoters of at least 3 organisms
Maximum number of matches:	1000

A match list with the organism, gene name, GeneID, position and strand of each model match.
Links to ElDorado and to EntrezGene are provided for each gene where a model match was found.

Example:

Organism	Gene	GeneID	Sequence	Model Name	Position	Strand
Genomatix homology group: 13535
Rattus norvegicus	Alb (albumin)	24186	GXP_294008	CEBP_HNF1_02	412 - 474	(+)
Mus musculus	Alb1 (albumin 1)	11657	GXP_152152	CEBP_HNF1_02	412 - 474	(+)
Bos taurus	ALB (albumin)	280717	GXP_1324534	CEBP_HNF1_02	398 - 461	(+)
Canis lupus familiaris	ALB (albumin)	403550	GXP_208626	CEBP_HNF1_02	391 - 454	(+)
Homo sapiens	ALB (albumin)	213	GXP_40794	CEBP_HNF1_02	391 - 454	(+)
Pan troglodytes	ALB (albumin)	461260	GXP_1440806	CEBP_HNF1_02	391 - 454	(+)
Macaca mulatta	ALB (albumin)	704892	GXP_1078447	CEBP_HNF1_02	392 - 455	(+)
Gallus gallus	ALB (albumin)	396197	GXP_1140646	CEBP_HNF1_02	351 - 418	(+)

Summary of the number of sequences searched and matches found.
Example:

A total of 8 matches was found in 1 homology groups.

Homology groups searched: 26190.
Sequences searched: 410256 (270320278 bp).

The model matches can be extracted in several ways, e.g. you can extract the sequence of the matches. Please select the matches in the match table by checking the select boxes in the column " Select Match" or by using the buttons below the match table. Per default all matches are selected.

Extraction Options
Sequence Extraction	You can extract the complete sequence or only the match positions (default) It is possible to extract further sequence positions upstream and downstream of the match positions. In this case you have to enter the number of additional basepairs into the box. Default value is ± 0 basepairs.
GeneID Extraction	The button "Extract GeneIDs" extracts the GeneIDs of the matching sequences for each model separately. The extracted GeneIDs can be e.g. used as input for GePS. The button "Extract GeneIDs by Chromosome" extracts the GeneIDs of the matching sequences for each chromosome separately.
Excel Extraction	The button "Export matches to EXCEL format" allows to export all information available in the match overview (like model name, sequence name and position of the model match) to a tab-delimited file. This file is saved to your local disk and can be opened directly with Microsoft Excel.

You can compare the results (GeneIDs of the promoter sequences) with a list of GeneIDs (e.g. from a ModelInspector search).

Compare results

Enter GeneIDs
Enter a list of GeneIDs separated by spaces, returns, or commas.

When you press the "Compare" button you will get the information which GeneIDs are common and which GeneIDs are specific either for your input list or for your result.

Compare results
Enter GeneIDs	Enter a list of GeneIDs separated by spaces, returns, or commas.

2. Detailed output

The second output file contains detailed information for each individual element of the model:

positions on the sequence and strand information
features of the element like sequence, length, matrix similarity, loop length, etc.

Example:

GXP_294008: Alb, GXL_247281, GeneID: 24186, Rattus norvegicus, albumin

Model: CEBP_HNF1_02 (410 - 472 (+))

Matrix element Model element	Position	Str	Sequence	Core sim. ---	Mat. sim. Model sim.	Distance to next element
V$CEBP/CEBPB.01	410 - 424	(+)	ATGATTTTGTAATGG	0.940	0.959	47 bp
V$HNF1/HNF1.02	456 - 472	(+)	GGTTAATGATCTACAGT	1.000	0.923	---

3. Statistics

The third output file contains a statistics of the model matches and detailed information for your own models:

Statistics of the number of matches for each model.
Detailed statistics for your own models, i.e. statistics of the found number of matches for each individual element and minimum and maximum distance to the following element.
'(+) strand matches' denotes the number of matches taken into account for model matches on the sense strand, '(-) strand matches' the number of matches considered for model matches on the antisense strand.

Example for the statistics:

Model Name	# matches	in # homology groups	in # organisms
Model Name	# matches	in # homology groups	Homo sapiens	Mus musculus	Rattus norvegicus	Gallus gallus	Canis familiaris	Bos taurus
CEBP_HNF1_02	6	1	1	1	1	1	1	1