Venn diagrams - Revision history

MaWin at 15:51, 3 December 2008

2008-12-03T15:51:43Z

MaWin at 15:51, 3 December 2008

2008-12-03T15:51:21Z

MaWin at 15:50, 3 December 2008

2008-12-03T15:50:46Z

Wideloache: /* Analysis */

2008-09-30T16:46:05Z

‎Analysis

Wideloache: /* Analysis */

2008-09-30T16:44:01Z

‎Analysis

Wideloache at 16:42, 30 September 2008

2008-09-30T16:42:53Z

Wideloache at 16:42, 30 September 2008

2008-09-30T16:42:45Z

Wideloache at 16:42, 30 September 2008

2008-09-30T16:42:18Z

Wideloache at 16:41, 30 September 2008

2008-09-30T16:41:32Z

Wideloache at 16:41, 30 September 2008

2008-09-30T16:41:17Z

← Older revision		Revision as of 15:51, 3 December 2008
Line 1:		Line 1:
−
−	~~<script type="text/javascript" src="http://www.google.com/jsapi"></script>~~
−	~~<script type="text/javascript">~~
−	~~google.load("visualization", "1", {packages:["barchart"]});~~
−	~~google.setOnLoadCallback(drawChart);~~
−	~~function drawChart() {~~
−	~~var data = new google.visualization.DataTable();~~
−	~~data.addColumn('string', 'Annotation');~~
−	~~data.addColumn('number', 'All three call the same stop codon index but rast has different start codon');~~
−	~~data.addColumn('number', 'All three call Different stop codon index');~~
−
−	~~data.addRows(3);~~
−	~~data.setValue(0, 0, 'JGI');~~
−	~~data.setValue(0, 1,650);~~
−	~~data.setValue(0, 2, 290);~~
−
−	~~data.setValue(1, 0, 'Rast');~~
−	~~data.setValue(1, 1,682);~~
−	~~data.setValue(1, 2,472);~~
−
−	~~data.setValue(2, 0, 'Manatee');~~
−	~~data.setValue(2, 1,655);~~
−	~~data.setValue(2, 2,242);~~
−
−
−
−
−	~~var chart = new google.visualization.BarChart(document.getElementById('chart_div'));~~
−	~~chart.draw(data, {width: 800, height: 300, is3D: true,titleX:"Average Gene Size (bp)", title: 'Average Gene Size Comparison'});~~
−	}
−	~~</script>~~
−
−
−
−	~~<div id="chart_div"></div>~~
−
−

	[[Image:ExactMatches.png\|thumb\|400px\|left\|'''Figure 1:''' Venn diagram showing the number of exact gene matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same start and stop index for a given gene.]][[Image:StopCodonMatches1.png\|thumb\|400px\|none\|'''Figure 2:''' Venn diagram showing the number of stop codon matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same stop index and strand (+/-) for a given gene.]]<br>		[[Image:ExactMatches.png\|thumb\|400px\|left\|'''Figure 1:''' Venn diagram showing the number of exact gene matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same start and stop index for a given gene.]][[Image:StopCodonMatches1.png\|thumb\|400px\|none\|'''Figure 2:''' Venn diagram showing the number of stop codon matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same stop index and strand (+/-) for a given gene.]]<br>

@@ Line 1: / Line 1: @@
      <script type="text/javascript" src="http://www.google.com/jsapi"></script>
      <script type="text/javascript">
@@ Line 31: / Line 30: @@
+       }
      </script>
-  </head>
-  <body>
      <div id="chart_div"></div>

← Older revision		Revision as of 15:50, 3 December 2008
Line 1:		Line 1:
		+
		+	<head>
		+	<script type="text/javascript" src="http://www.google.com/jsapi"></script>
		+	<script type="text/javascript">
		+	google.load("visualization", "1", {packages:["barchart"]});
		+	google.setOnLoadCallback(drawChart);
		+	function drawChart() {
		+	var data = new google.visualization.DataTable();
		+	data.addColumn('string', 'Annotation');
		+	data.addColumn('number', 'All three call the same stop codon index but rast has different start codon');
		+	data.addColumn('number', 'All three call Different stop codon index');
		+
		+	data.addRows(3);
		+	data.setValue(0, 0, 'JGI');
		+	data.setValue(0, 1,650);
		+	data.setValue(0, 2, 290);
		+
		+	data.setValue(1, 0, 'Rast');
		+	data.setValue(1, 1,682);
		+	data.setValue(1, 2,472);
		+
		+	data.setValue(2, 0, 'Manatee');
		+	data.setValue(2, 1,655);
		+	data.setValue(2, 2,242);
		+
		+
		+
		+
		+	var chart = new google.visualization.BarChart(document.getElementById('chart_div'));
		+	chart.draw(data, {width: 800, height: 300, is3D: true,titleX:"Average Gene Size (bp)", title: 'Average Gene Size Comparison'});
		+	}
		+	</script>
		+	</head>
		+
		+	<body>
		+	<div id="chart_div"></div>
		+	</body>
		+
		+
		+
	[[Image:ExactMatches.png\|thumb\|400px\|left\|'''Figure 1:''' Venn diagram showing the number of exact gene matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same start and stop index for a given gene.]][[Image:StopCodonMatches1.png\|thumb\|400px\|none\|'''Figure 2:''' Venn diagram showing the number of stop codon matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same stop index and strand (+/-) for a given gene.]]<br>		[[Image:ExactMatches.png\|thumb\|400px\|left\|'''Figure 1:''' Venn diagram showing the number of exact gene matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same start and stop index for a given gene.]][[Image:StopCodonMatches1.png\|thumb\|400px\|none\|'''Figure 2:''' Venn diagram showing the number of stop codon matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same stop index and strand (+/-) for a given gene.]]<br>

← Older revision		Revision as of 16:46, 30 September 2008
Line 3:		Line 3:

	==Analysis==		==Analysis==
−	The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). This means that the gene calls in Rast significantly differed from the gene calls made by JGI and Manatee. However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the stop codons were usually ~~called~~ the same ~~by Rast~~, the start codons that Rast called frequently differed from ~~Manatee or JGI~~.	+	The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). This means that the gene calls in Rast significantly differed from the gene calls made by JGI and Manatee. However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the Rast's stop codons calls were usually the same as JGI and Manatee, the start codons that Rast called frequently differed from the other two annotations. This often resulted in Rast predicting longer genes, as can be view in this [[Gene Length Histograms\|histogram]].

← Older revision		Revision as of 16:44, 30 September 2008
Line 3:		Line 3:

	==Analysis==		==Analysis==
−	The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the stop codons were usually called the same by Rast, the start codons that Rast called frequently differed from Manatee or JGI.	+	The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). This means that the gene calls in Rast significantly differed from the gene calls made by JGI and Manatee. However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the stop codons were usually called the same by Rast, the start codons that Rast called frequently differed from Manatee or JGI.

← Older revision		Revision as of 16:42, 30 September 2008
Line 3:		Line 3:

	==Analysis==		==Analysis==
−	The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the stop codons were usually called the same by Rast, the start codons that Rast called frequently differed from Manatee or JGI.	+	The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the stop codons were usually called the same by Rast, the start codons that Rast called frequently differed from Manatee or JGI.

← Older revision		Revision as of 16:42, 30 September 2008
Line 2:		Line 2:


−	Analysis: The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the stop codons were usually called the same by Rast, the start codons that Rast called frequently differed from Manatee or JGI.	+	==Analysis==
		+	The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the stop codons were usually called the same by Rast, the start codons that Rast called frequently differed from Manatee or JGI.

← Older revision		Revision as of 16:41, 30 September 2008
Line 1:		Line 1:
−	[[Image:ExactMatches.png\|thumb\|400px\|~~none~~\|Figure 1: Venn diagram showing the number of exact gene matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same start and stop index for a given gene.]][[Image:StopCodonMatches1.png\|thumb\|400px\|none\|Figure 2: Venn diagram showing the number of stop codon matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same stop index and strand (+/-) for a given gene.]]<br>	+	[[Image:ExactMatches.png\|thumb\|400px\|left\|Figure 1: Venn diagram showing the number of exact gene matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same start and stop index for a given gene.]][[Image:StopCodonMatches1.png\|thumb\|400px\|none\|Figure 2: Venn diagram showing the number of stop codon matches across the 3 annotations. Regions that overlap denote that the overlapping annotations called the same stop index and strand (+/-) for a given gene.]]<br>


	Analysis: The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the stop codons were usually called the same by Rast, the start codons that Rast called frequently differed from Manatee or JGI.		Analysis: The major trend that can be noted by comparing these 2 Venn diagrams involves the Rast annotation. In the Figure 1, JGI and Manatee overlapped with each other (985+1471=2456) significantly more than 3 annotations overlapped collectively (1471). However, in Figure 2 this trend disappears. This is likely due to the use of more alternative start codons by Rast. While the stop codons were usually called the same by Rast, the start codons that Rast called frequently differed from Manatee or JGI.