Difference between revisions of "GTRD"

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(Repository structure)
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===Repository structure===
 
===Repository structure===
 +
GTRD is organized in hierarchical [Repository].
 +
 
[[File:gtrd_repository.png|GTRD repository]]
 
[[File:gtrd_repository.png|GTRD repository]]
  
 +
The GTRD/Data folder contains following items:
 +
*experiments - ChIP-seq experiments metainformation
 +
*sequences - Raw ChIP-seq reads in fastq.gz format
 +
*alignments - ChIP-seq read alignments
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*peaks - ChIP-seq peaks identified by MACS and SISSRS peak callers
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*matrices - Position weight matrices for transcription factor binding sites
 +
*site models - Models for recognition of transcription factor binding sites
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*statistics - Summary GTRD statistics
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*views - TFClass centric view of GTRD data avalable as {{Type link|tree-table}}s
  
For convenience some views are available as {{Type link|tree-table}}s.
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GTRD/Dictionaries/classification is [[http://www.edgar-wingender.de/huTF_classification.html TFClass]] classification tree used by GTRD to reference transcription factors.

Revision as of 17:24, 2 July 2013

GTRD (Gene Transcription Regulation Database) is a database of transcription factor binding sites identified from ChIP-seq experiments. GTRD analyzes freely avalable ChIP-seq experiments from literature, GEO, SRA and ENCODE databases.

The web interface to GTRD is available here.

Contents

Database statistics

GTRD uses 2417 ChIP-seq experiments for 470 distinct sequence specific transcription factors.
ChIP-seq experiments by species
Most of ChIP-seq experiments (1638) have corresponding control experiment.
Control experiments

General statistics:

Object type Total count Per ChIP-seq experiment
ChIP-seq reads 80.808E9 34.937E6
Reads aligned 58.848E9 25.675E6
ChIP-seq peaks 59.515E6 32899

In average each transcription factor is measured in 4.07 ChIP-seq experiments, but 284 (60%) transcription factors measured only in one experiment.

The ten most studied transcription factors listed bellow:

Transcription Factor Number of ChIP-seq experiments
CTCF 195
c-Myc 45
ERα 44
NRSF 37
C/EBPβ 37
GATA-1 33
NF-κB p65 30
Max 30
PU.1 29
GR 24

The detailed database statistics available in the GTRD#Web interface

Database structure

The metadata concerning GTRD is stored in MySQL tables.

Each ChIP-seq experiment has a row in 'chip_experiments' table, which assigns id and stores basic information about experiment. 'chip_experiments' table has following structure:

Column Description Example value
id Unique experiment identifier EXP000489
antibody Antibody used in chromatin immunoprecipitation sc-345
tfClassId Id in TFClass[1] database of target transcription factor, NULL for control experiments 6.2.1.0.1
cell_line Studied cell line HeLa S3
specie Specie latin name Homo sapiens
treatment Cell treatment or conditions IFN gamma
control_id Id of control experiment, NULL for control experiments or experiments without control EXP000490

The links to external databases stored in 'external_refs' table:

Column Description Example values
id Experiment identifier EXP000489
external_db External database name GEO or PUBMED or ENCODE or SRA
external_db_id Identifier in external database GSM320736

GTRD uses following object identifiers:

Template Object type Example
EXPXXXXXX ChIP-seq experiment EXP000489
READSXXXXXX Collection of ChIP-seq reads READS000770
ALIGNSXXXXXX Collection of read alignments ALIGNS010001
PEAKSXXXXXX Collection of ChIP-seq peaks PEAKS010000

The relationship between these objects is provided by 'hub' table:

Column Description Example values
input Input object identifier READS000770
input_type Type of input object ReadsGTRDType
output Output object identifier EXP000489
output_type Type of output object ExperimentGTRDType

ChIP-seq reads, alignments and peaks links to experiments with hub table in the following way:

input input_type output output_type
READS000770 ReadsGTRDType EXP000489 ExperimentGTRDType
READS000771 ReadsGTRDType EXP000489 ExperimentGTRDType
READS000772 ReadsGTRDType EXP000489 ExperimentGTRDType
READS000773 ReadsGTRDType EXP000489 ExperimentGTRDType
READS000774 ReadsGTRDType EXP000489 ExperimentGTRDType
READS000775 ReadsGTRDType EXP000489 ExperimentGTRDType
ALIGNS010001 AlignmentsGTRDType EXP000489 ExperimentGTRDType
PEAKS010000 PeaksGTRDType EXP000489 ExperimentGTRDType


Web interface

This page or section is a stub. Please add screenshots here!

Web interface to GTRD is available here. It provides capabilities for searching and browsing GTRD.

Start page

Start page contains search box and the links to browse all experiments in the repository tree, explore databases statistics and transcription factor classification tree.

GTRD start page

Search capabilities

The ChIP-seq experiments contained in GTRD can be queried from the search box on the Start page. GTRD uses Lucene engine for indexing and quering ChIP-seq experiments that provides rich syntax for searching. The search can be performed by transcription factor(name or class), cell line, antibody or treatment/conditions.

Search GTRD

For example, to search for stat transcription factors enter stat* in the search field and press enter. You can restrict query to hela cells treated with interferon with following query:

 tfTitle:stat* AND cellLine:hela AND treatment:IFN

The list of matching ChIP-seq experiments will appear in the 'Search result' tab. Select one of them to view detailed ChIP-seq experiment information in the 'Info' tab. The 'Info' tab also provides links to the experiment data: reads, alignments and peaks.

Open ChIP-seq peaks

To view peaks or alignments click the link in the ChIP-seq experiment 'Info' tab, the Type-track-icon.png track will be opened as table. The Type-track-icon.png track can be exported by pressing 'Export' button or opened in the Genome browser by pressing 'Open as track' button in the General_control_panel.

Repository structure

GTRD is organized in hierarchical [Repository].

GTRD repository

The GTRD/Data folder contains following items:

  • experiments - ChIP-seq experiments metainformation
  • sequences - Raw ChIP-seq reads in fastq.gz format
  • alignments - ChIP-seq read alignments
  • peaks - ChIP-seq peaks identified by MACS and SISSRS peak callers
  • matrices - Position weight matrices for transcription factor binding sites
  • site models - Models for recognition of transcription factor binding sites
  • statistics - Summary GTRD statistics
  • views - TFClass centric view of GTRD data avalable as Type-tree-table-icon.png tree-tables

GTRD/Dictionaries/classification is [TFClass] classification tree used by GTRD to reference transcription factors.

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