GTRD - Revision history

Semyonk@dote.ru at 07:13, 22 October 2019

2019-10-22T07:13:26Z

Ivan@dote.ru: /* Search capabilities */

2018-10-23T10:51:36Z

‎Search capabilities

Semyonk@dote.ru: /* Web interface */

2018-10-23T07:20:50Z

‎Web interface

Shrus79@gmail.com at 07:08, 23 October 2018

2018-10-23T07:08:05Z

Shrus79@gmail.com at 06:10, 23 October 2018

2018-10-23T06:10:52Z

Shrus79@gmail.com at 06:10, 23 October 2018

2018-10-23T06:10:02Z

Semyonk@dote.ru: /* Start page */

2018-10-22T11:43:32Z

‎Start page

Semyonk@dote.ru: /* Repository structure */

2018-10-22T11:39:20Z

‎Repository structure

Semyonk@dote.ru: /* Repository structure */

2018-10-22T11:34:35Z

‎Repository structure

Semyonk@dote.ru: /* Repository structure */

2018-10-22T11:30:32Z

‎Repository structure

@@ Line 9: / Line 9: @@
 ChIP-seq processing pipeline included the following steps:
 * sequenced reads were aligned to the corresponding reference genome using Bowtie2;
-* peaks were identified using MACS, SISSR, GEM and PICS peak callers;
+* 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.

@@ Line 214: / Line 214: @@
 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
 The list of matching ChIP-seq experiments will appear in the 'Search result' tab.

← Older revision		Revision as of 07:20, 23 October 2018
Line 194:		Line 194:

	==Web interface==		==Web interface==
−	~~{{stub\|screenshots}}~~

	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].

@@ Line 210: / Line 210: @@
 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.
-The search can be performed by transcription factor(name or uniprot ID), cell line, antibody or treatment/conditions.
+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 enter stat* in the search field and press enter.
+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 with following query:
+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

@@ Line 1: / Line 1: @@
 [[Category:Databases]]
-'''Gene Transcription Regulation Database''' ([http://gtrd.biouml.org GTRD]) is a database of transcription factor (TF) binding sites (TFBSs) 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:
+'''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
 * [http://www.ncbi.nlm.nih.gov/geo/ GEO]

@@ Line 1: / Line 1: @@
 [[Category:Databases]]
-'''Gene Transcription Regulation Database''' ([http://gtrd.biouml.org GTRD]) is a database of transcription factor binding sites identified from ChIP-seq experiments that were systematically collected and uniformly processed using special workflow (pipeline) for BioUML platform. Raw ChIP-seq data and experiment information were collected from:
+'''Gene Transcription Regulation Database''' ([http://gtrd.biouml.org GTRD]) is a database of transcription factor (TF) binding sites (TFBSs) 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
 * [http://www.ncbi.nlm.nih.gov/geo/ GEO]
@@ Line 6: / Line 6: @@
 * [http://genome.ucsc.edu/ENCODE/ ENCODE].
-Initial ChIP-seq and DNase-seq raw data were uniformly processed using specially developed workflow (pipeline) for BioUML platform.
+Initial ChIP-seq and DNase-seq raw data were uniformly processed using specially developed workflow (pipeline) for the BioUML platform.
-ChIP-seq processing pipeline:
+ChIP-seq processing pipeline included the following steps:
-* sequenced reads were aligned to reference genome using Bowtie2;
+* sequenced reads were aligned to the corresponding reference genome using Bowtie2;
 * peaks were identified using MACS, 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:
+DNase-seq processing pipeline included the following steps:
-* sequenced reads were aligned to reference genome using Bowtie2;
+* sequenced reads were aligned to the corresponding reference genome using Bowtie2;
 * regions of open chromatin were identified using MACS2 and Hotspot2;
-* to reveal de novo putative protein-DNA interactions digital genomic footprinting tool Wellington was used.
+* de novo putative protein-DNA interactions were revealed using a digital genomic footprinting tool Wellington.
 [[GTRD_Workflow|Learn more about GTRD build process]]
@@ Line 22: / Line 22: @@
 ==Database statistics (18.06 version)==
-GTRD uses 17485 ChIP-seq experiments correspond to 2399 uniprot IDs. [[File:GTRD statistics-by-species3.png|thumb|ChIP-seq experiments by species]]
+GTRD uses 17485 ChIP-seq experiments corresponding to 2399 UniProt IDs. [[File:GTRD statistics-by-species3.png|thumb|ChIP-seq experiments by species]]
-Most of ChIP-seq experiments (79.2%) have corresponding control experiment. [[File:GTRD statistics-control3.png|thumb|Control experiments]]
+Most of ChIP-seq experiments (79.2%) have corresponding control experiments. [[File:GTRD statistics-control3.png|thumb|Control experiments]]
 General statistics:
@@ Line 38: / Line 38: @@
 |}
-In average each TF has been measured in 7.28 ChIP-seq experiments, 52% of TFs have been measured in more than one experiment. [[File:GTRD tf-statistics-by-species3.png|thumb|Transription factors by species]]
+In average, each TF has been measured in 7.28 ChIP-seq experiments, 52% of TFs have been measured in more than one experiment. [[File:GTRD tf-statistics-by-species3.png|thumb|Transription factors by species]]
-The ten most studied transcription factors are listed bellow:
+Ten most studied TFs are listed bellow:
 {| class="wikitable"
@@ Line 73: / Line 73: @@
 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 following structure:
+'chip_experiments' table has the following structure:
 {| class="wikitable"
@@ Line 96: / Line 96: @@
 |}
-'dnase_experiments' table has following structure:
+'dnase_experiments' table has the following structure:
 {| class="wikitable"
@@ Line 124: / Line 124: @@
 |}
-GTRD uses following object identifiers:
+GTRD uses the following object identifiers:
 {| class="wikitable"
 |-
@@ Line 146: / Line 146: @@
 |}
-The relationship between these objects is provided by 'hub' table:
+The relationship between these objects is provided by a 'hub' table:
 {| class="wikitable"
 |-

@@ Line 200: / Line 200: @@
 ===Start page===
-Start page contains search box and the links to browse all experiments in the repository tree, documentation, help (wiki pages) and transcription factor classification tree.
+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.
-[[File:gtrd_startpage3.png|GTRD start page]]
+[[File:gtrd_startpage3.png|GTRD start page|1100px]]
 ===Search capabilities===

@@ Line 225: / Line 225: @@
 GTRD is organized in hierarchical [[Repository]].
-[[File:gtrd_repository3.png|GTRD repository|100x150px]]
+[[File:gtrd_repository3.png|GTRD repository|235x307px]]
 The GTRD/Data folder contains following items:
@@ Line 233: / Line 233: @@
 *experiments - ChIP-seq experiments metainformation
 *peaks - ChIP-seq and DNase-seq peaks identified by peak callers
 GTRD/Dictionaries/classification is [http://www.edgar-wingender.de/huTF_classification.html TFClass] classification tree used by GTRD to reference transcription factors.
 GTRD/Dictionaries/cells is a collection of cells and tissues used by GTRD

@@ Line 232: / Line 232: @@
 *clusters - ChIP-seq-derived meta-clusters
 *experiments - ChIP-seq experiments metainformation
 *peaks - ChIP-seq and DNase-seq peaks identified by peak callers
 *views - TFClass centric view of GTRD data avalable as {{Type link|tree-table}}s