Difference between revisions of "GTRD"
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[[Category:Databases]] | [[Category:Databases]] | ||
| − | '''Gene Transcription Regulation Database''' ([http://gtrd.biouml.org GTRD]) is a database of transcription factor (TF) binding sites | + | '''Gene Transcription Regulation Database''' ([http://gtrd.biouml.org GTRD]) is a database of transcription factor (TF) binding sites identified from ChIP-seq experiments that were systematically collected and uniformly processed using a special workflow (pipeline) for a BioUML platform (http://www.biouml.org). Raw ChIP-seq data and experiment information were collected from: |
* literature | * literature | ||
* [http://www.ncbi.nlm.nih.gov/geo/ GEO] | * [http://www.ncbi.nlm.nih.gov/geo/ GEO] | ||
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ChIP-seq processing pipeline included the following steps: | ChIP-seq processing pipeline included the following steps: | ||
* sequenced reads were aligned to the corresponding reference genome using Bowtie2; | * sequenced reads were aligned to the corresponding reference genome using Bowtie2; | ||
| − | * peaks were identified using | + | * peaks were identified using MACS2, SISSR, GEM and PICS peak callers; |
* peaks computed for the same TF and peak calling method, but different experiment conditions (e.g., cell line, treatment, etc.) were joined into clusters; | * peaks computed for the same TF and peak calling method, but different experiment conditions (e.g., cell line, treatment, etc.) were joined into clusters; | ||
* clusters for the same TF revealed by different peak calling methods were joined into metaclusters. | * clusters for the same TF revealed by different peak calling methods were joined into metaclusters. | ||
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==Web interface== | ==Web interface== | ||
| − | |||
Web interface to GTRD is available [http://gtrd.biouml.org/bioumlweb/gtrd.html here]. | Web interface to GTRD is available [http://gtrd.biouml.org/bioumlweb/gtrd.html here]. | ||
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The ChIP-seq experiments contained in GTRD can be queried from the search box on the Start page. | The ChIP-seq experiments contained in GTRD can be queried from the search box on the Start page. | ||
GTRD uses [http://en.wikipedia.org/wiki/Lucene Lucene] engine for indexing and quering ChIP-seq experiments that provides rich [http://lucene.apache.org/core/2_9_4/queryparsersyntax.html syntax] for searching. | GTRD uses [http://en.wikipedia.org/wiki/Lucene Lucene] engine for indexing and quering ChIP-seq experiments that provides rich [http://lucene.apache.org/core/2_9_4/queryparsersyntax.html syntax] for searching. | ||
| − | The search can be performed by transcription factor(name or | + | The search can be performed by transcription factor(name or UniProt ID), cell line, antibody or treatment/conditions. |
| − | For example, to search for STAT transcription factors | + | For example, to search for STAT transcription factors you should input 'stat*' in the search field and press 'Enter'. |
| − | You can restrict query to HeLa cells treated with interferon | + | You also can restrict the query to a certain cell line and treatment, e.g. to HeLa cells treated with interferon, using the following query: |
tfTitle:stat* AND cell:hela AND treatment:IFN | tfTitle:stat* AND cell:hela AND treatment:IFN | ||
| + | Similarly, it is possible to search by publication author, year or title. To search by full article title, quote it: | ||
| + | "Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing." | ||
| + | To search by author or publication date, use "articles:" prefix. For example to search for experiments authored by Snyder in 2007: | ||
| + | articles:Snyder AND articles:2007 | ||
The list of matching ChIP-seq experiments will appear in the 'Search result' tab. | The list of matching ChIP-seq experiments will appear in the 'Search result' tab. | ||
Latest revision as of 14:13, 22 October 2019
Gene Transcription Regulation Database (GTRD) is a database of transcription factor (TF) binding sites identified from ChIP-seq experiments that were systematically collected and uniformly processed using a special workflow (pipeline) for a BioUML platform (http://www.biouml.org). Raw ChIP-seq data and experiment information were collected from:
Initial ChIP-seq and DNase-seq raw data were uniformly processed using specially developed workflow (pipeline) for the BioUML platform. ChIP-seq processing pipeline included the following steps:
- sequenced reads were aligned to the corresponding reference genome using Bowtie2;
- peaks were identified using MACS2, SISSR, GEM and PICS peak callers;
- peaks computed for the same TF and peak calling method, but different experiment conditions (e.g., cell line, treatment, etc.) were joined into clusters;
- clusters for the same TF revealed by different peak calling methods were joined into metaclusters.
DNase-seq processing pipeline included the following steps:
- sequenced reads were aligned to the corresponding reference genome using Bowtie2;
- regions of open chromatin were identified using MACS2 and Hotspot2;
- de novo putative protein-DNA interactions were revealed using a digital genomic footprinting tool Wellington.
Learn more about GTRD build process
GTRD database is freely available for non-commercial organizations.
Contents |
[edit] Database statistics (18.06 version)
GTRD uses 17485 ChIP-seq experiments corresponding to 2399 UniProt IDs.
General statistics:
| Object type | Total count | Per ChIP-seq experiment |
|---|---|---|
| ChIP-seq reads | 719.3 × 109 | 41.1 × 106 |
| Reads aligned | 539.8 × 109 | 30.9 × 106 |
| ChIP-seq peaks | >1.1 × 109 | depends on peak caller |
Ten most studied TFs are listed bellow:
| uniprot ID | Transcription Factor | Species | Number of ChIP-seq experiments |
|---|---|---|---|
| P49711 | CTCF | Homo sapiens | 432 |
| P03372 | SR1 | Homo sapiens | 280 |
| P10275 | ANDR | Homo sapiens | 259 |
| Q61164 | CTCF | Mus musculus | 255 |
| P17433 | SPI1 | Mus musculus | 156 |
| P55317 | FOXA1 | Homo sapiens | 125 |
| P01106 | MYC | Homo sapiens | 122 |
| P28033 | CEBPB | Mus musculus | 100 |
| Q04206 | TF65 | Homo sapiens | 93 |
| P04150 | GCR | Homo sapiens | 90 |
[edit] Database structure
The metadata concerning GTRD is stored in MySQL tables.
Each ChIP-seq and DNase-seq experiment has a row in 'chip_experiments' or 'dnase-experiments' table, respectively, which assigns id and stores basic information about experiment. 'chip_experiments' table has the following structure:
| Column | Description | Example value |
|---|---|---|
| id | Unique experiment identifier | EXP000489 |
| antibody | Antibody used in chromatin immunoprecipitation | sc-345 |
| specie | Species 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 |
| cell_id | Studied cell line ID | 423 |
| experiment_type | unspecified | |
| tf_uniprot_id | Protein id in Uniprot database | P42224 |
'dnase_experiments' table has the following structure:
| Column | Description | Example value |
|---|---|---|
| id | Unique experiment identifier | DEXP000044 |
| organism | Species latin name | Homo sapiens |
| treatment | Cell treatment or conditions | 100nM dexamethasone (CHEBI:41879) for 6 hour |
| cell_id | Studied cell line ID | 38 |
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 the following object identifiers:
| Template | Object type | Example |
|---|---|---|
| EXPXXXXXX | ChIP-seq experiment | EXP000489 |
| READSXXXXXX | Collection of ChIP-seq reads | READS000770 |
| ALIGNSXXXXXX | Collection of ChIP-seq reads alignments | ALIGNS010001 |
| PEAKSXXXXXX | Collection of DNase-seq peaks | PEAKS010000 |
| DEXPXXXXXX | DNase-seq experiment | DEXP000044 |
| DREADSXXXXXX | Collection of DNase-seq reads | DREADS000232 |
| DALIGNSXXXXXX | Collection of DNase-seq reads alignments | DALIGNS000044 |
| DPEAKSXXXXXX | Collection of DNase-seq peaks | DPEAKS000044 |
The relationship between these objects is provided by a '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 and DNase-seq reads, alignments and peaks links to experiments with hub table in the following way:
| input | input_type | output | output_type | specie |
|---|---|---|---|---|
| READS000770 | ReadsGTRDType | EXP000489 | ExperimentGTRDType | Homo sapiens |
| READS000771 | ReadsGTRDType | EXP000489 | ExperimentGTRDType | Homo sapiens |
| READS000772 | ReadsGTRDType | EXP000489 | ExperimentGTRDType | Homo sapiens |
| READS000773 | ReadsGTRDType | EXP000489 | ExperimentGTRDType | Homo sapiens |
| READS000774 | ReadsGTRDType | EXP000489 | ExperimentGTRDType | Homo sapiens |
| READS000775 | ReadsGTRDType | EXP000489 | ExperimentGTRDType | Homo sapiens |
| ALIGNS033052 | AlignmentsGTRDType | EXP000489 | ExperimentGTRDType | Homo sapiens |
| PEAKS033050 | PeaksGTRDType | EXP000489 | ExperimentGTRDType | Homo sapiens |
| DALIGNS000044 | DNaseAlignments | DEXP000044 | DNaseExperiment | Homo sapiens |
| DPEAKS000044 | DNasePeaks | DEXP000044 | DNaseExperiment | Homo sapiens |
| DREADS000232 | DNaseReads | DEXP000044 | DNaseExperiment | Homo sapiens |
| DREADS000233 | DNaseReads | DEXP000044 | DNaseExperiment | Homo sapiens |
| DREADS000234 | DNaseReads | DEXP000044 | DNaseExperiment | Homo sapiens |
| DREADS000235 | DNaseReads | DEXP000044 | DNaseExperiment | Homo sapiens |
[edit] Web interface
Web interface to GTRD is available here. It provides capabilities for searching and browsing GTRD.
[edit] Start page
Start page contains search boxes and the links to browse all experiments in the repository tree, documentation, help (wiki pages) and transcription factor classification tree.
[edit] 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 UniProt ID), cell line, antibody or treatment/conditions.
For example, to search for STAT transcription factors you should input 'stat*' in the search field and press 'Enter'. You also can restrict the query to a certain cell line and treatment, e.g. to HeLa cells treated with interferon, using the following query:
tfTitle:stat* AND cell:hela AND treatment:IFN
Similarly, it is possible to search by publication author, year or title. To search by full article title, quote it:
"Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing."
To search by author or publication date, use "articles:" prefix. For example to search for experiments authored by Snyder in 2007:
articles:Snyder AND articles:2007
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 information box. The information box also provides links to the experiment data: reads, alignments and peaks.
To view peaks or alignments click the link in the ChIP-seq experiment information box, the 
track will be opened as table. The 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.
[edit] Repository structure
GTRD is organized in hierarchical Repository.
The GTRD/Data folder contains following items:
- DNase experiments - DNase-seq experiments metainformation
- alignments - ChIP-seq read alignments
- clusters - ChIP-seq-derived meta-clusters
- experiments - ChIP-seq experiments metainformation
- peaks - ChIP-seq and DNase-seq peaks identified by peak callers
GTRD/Dictionaries/classification is TFClass classification tree used by GTRD to reference transcription factors. GTRD/Dictionaries/cells is a collection of cells and tissues used by GTRD
