Promoter Analysis - Revision history

Smith: /* Prerequisites */

2014-01-23T00:19:25Z

‎Prerequisites

2014-01-23T00:17:43Z

‎Prerequisites

2014-01-23T00:15:05Z

‎Prerequisites

2014-01-23T00:13:31Z

‎Prerequisites

2014-01-23T00:08:27Z

2014-01-10T21:41:14Z

‎Add TF

2014-01-10T21:21:41Z

‎Add TF

2014-01-10T21:21:01Z

‎Add TF

2013-09-18T22:14:21Z

‎Background sequence and scoring threshold determination

2013-07-16T19:42:01Z

‎Running the scan

← Older revision		Revision as of 00:19, 23 January 2014
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−	[[Image:~~T_SequenceRetriever_CDH2_seq_in_proj_folder-2~~.png]]	+	[[Image:Promoter_example_in_Workspace.png]]

	==Running the scan==		==Running the scan==

← Older revision		Revision as of 00:17, 23 January 2014
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	[[Image:Sequence_Retriever_CDH2.png\|{{ImageMaxWidth}}]]		[[Image:Sequence_Retriever_CDH2.png\|{{ImageMaxWidth}}]]

−	10. Once the sequence has been retrieved, check the box next to the sequence and then hit the button "Add to Workspace". We now have the genomic sequence available for other components to use.	+	10. Once the sequence has been retrieved, check the box next to the sequence and then hit the button "Add to Workspace". You will be prompted to enter a name for the sequence. We now have the genomic sequence available for other components to use.

@@ Line 225: / Line 225: @@
 . When prompted, associate the HG-U95Av2 annotation file.
-. In the Markers component, search for the gene name "CDH2" using the '''Find Next''' button.  On this chip type, marker 2053_at represents the CDH2 gene.
+. In the Markers component, search for the gene "CDH2".  On this chip type, marker 2053_at represents the CDH2 gene.
 . You can double-click on the marker to add it to the default "Selection" set.  Or you can right-click on it and add it to a named set, such as "Cadherins".  This is depicted below.

@@ Line 217: / Line 217: @@
 The Promoter component is only available when a sequence has been loaded, either from disk or for example using the Sequence Retriever component to obtain genomic sequence.
-For this example, we will obtain upstream genomic sequence for CDH2, the N-Cadherin gene.  However, using the Sequence Retriever component requires that a microarray dataset and its annotations be loaded.  Here, we will use the JB-ccmp_0120.txt file, which is an Affymetrix HG-U95Av2 MAS5 format text file and is part of the geWorkbench [http://wiki.c2b2.columbia.edu/workbench/index.php/Download#Tutorial_data tutorial dataset].
+For this example, we will obtain upstream genomic sequence for CDH2, the N-Cadherin gene.  However, using the Sequence Retriever component requires that a microarray dataset and its annotations be loaded.  Here, we will use the JB-ccmp_0120.txt file, which is an Affymetrix HG-U95Av2 '''MAS5''' format text file and is part of the geWorkbench distribution example data, found in data\cardiogenomics.med.harvard.edu.
 The Affymetrix HG-U95Av2 annotation file can be obtain from the Affymetrix website.  Please see instructions on the [http://wiki.c2b2.columbia.edu/workbench/index.php/FAQ#Q._Where_can_I_obtain_the_latest_annotation_files_for_my_microarray_platform.3F geWorkbench FAQ].

@@ Line 17: / Line 17: @@
 ==Prerequisites==
 * To use the Promoter component, first check that it has been loaded in the  Component Configuration Manager.
-* The Promoter component appears when a data node of type "sequence" has been loaded in the Project Folders component.
+* The Promoter component appears when a data node of type "sequence" has been loaded in the [[Workspace]].
 * The Promoter component appears in the upper-right quadrant of geWorkbench, in the "Visual Area".
@@ Line 221: / Line 221: @@
 The Affymetrix HG-U95Av2 annotation file can be obtain from the Affymetrix website.  Please see instructions on the [http://wiki.c2b2.columbia.edu/workbench/index.php/FAQ#Q._Where_can_I_obtain_the_latest_annotation_files_for_my_microarray_platform.3F geWorkbench FAQ].
-. In the Project Folders component, load the file JB-ccmp_0120.txt as type  MAS5/GCOS.
+. In the [[Workspace]], load the file JB-ccmp_0120.txt as type  MAS5/GCOS.
 . When prompted, associate the HG-U95Av2 annotation file.
@@ Line 243: / Line 243: @@
 [[Image:Sequence_Retriever_CDH2.png|{{ImageMaxWidth}}]]
-. Once the sequence has been retrieved, check the box next to the sequence and then hit the button "Add to Project".  We now have the genomic sequence available for other components to use.
+. Once the sequence has been retrieved, check the box next to the sequence and then hit the button "Add to Workspace".  We now have the genomic sequence available for other components to use.

← Older revision		Revision as of 21:41, 10 January 2014
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	Because the normalization step uses the count total (sequences aligned to generate the profile), loading a frequency matrix is not currently supported.		Because the normalization step uses the count total (sequences aligned to generate the profile), loading a frequency matrix is not currently supported.
		+
		+	New profiles are loaded for the current session of geWorkbench only; they will not persist when geWorkbench is restarted.

	====Save====		====Save====

@@ Line 69: / Line 69: @@
 ====Add TF====
-The profile should consist of a tab delimited series of counts, one for each position in the profile.  It should could four lines, in the order A, C, G, T.  There are no header lines or row labels, just the numeric matrix.  For example, here is a profile showing the first six columns:
+The profile should consist of a tab delimited series of counts, one for each position in the profile (JASPAR format).  It should could four lines, in the order A, C, G, T.  There are no header lines or row labels, just the numeric matrix.  For example, here is a profile showing the first six columns:
   12 0  0  1  0

@@ Line 128: / Line 128: @@
 A background sequence is used to estimate an appropriate scoring threshold.  This background can be generated in two ways.
 # determine base composition of input sequence and from this generate random sequence.
-# (13K) - use a set of 13,000 promoter sequences as background.
+# (13K) - use a set of 13,000 promoter sequences as background (obtained from the PRIMA homepage http://acgt.cs.tau.ac.il/prima/).
 * The length of background sequence scanned is given by 1000*Iterations/PValue.

@@ Line 255: / Line 255: @@
 . Double-click on the TFAP2A entry to move it down to the search list.
-[[Image:Promoter_CDH2_AP2_2000updn_setup_logo.png]]
+[[Image:Promoter_CDH2_AP2_2000updn_setup_logo.png|{{ImageMaxWidth}}]]
 . Hit the "'''Scan'''" button.  The result is displayed in the '''Sequence''' tab of the Promoter component as shown here.
-[[Image:Promoter_Result_CDH2_Sequence_View.png]]
+[[Image:Promoter_Result_CDH2_Sequence_View.png|{{ImageMaxWidth}}]]
 . Setting the View to Full Sequence shows the hits in white on the sequence. Red arrows indicate whether the hit is to the forward (right arrow) or reverse (complementary) (left-arrow) strand.
@@ Line 268: / Line 268: @@
-[[Image:Promoter_Result_CDH2_Parameter_View.png]]
+[[Image:Promoter_Result_CDH2_Parameter_View.png|{{ImageMaxWidth}}]]
 =References=