Gene Length Histograms - Revision history

MaWin at 15:48, 3 December 2008

2008-12-03T15:48:53Z

2008-12-03T15:48:08Z

2008-09-30T20:48:24Z

2008-09-30T20:46:54Z

2008-09-30T18:27:58Z

2008-09-30T18:27:35Z

2008-09-30T18:27:10Z

2008-09-30T18:21:35Z

2008-09-30T18:19:24Z

2008-09-30T17:58:18Z

← Older revision		Revision as of 15:48, 3 December 2008
Line 30:		Line 30:
	\| 3097 \|\| 2898 \|\| 3254		\| 3097 \|\| 2898 \|\| 3254
	\|}		\|}
−	~~<html>~~
−	~~<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>~~
−	~~</html>~~

← Older revision		Revision as of 15:48, 3 December 2008
Line 30:		Line 30:
	\| 3097 \|\| 2898 \|\| 3254		\| 3097 \|\| 2898 \|\| 3254
	\|}		\|}
		+	<html>
		+	<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>
		+	</html>

@@ Line 2: / Line 2: @@
 [[Image:RastHistogram.png|400px|none]]
 [[Image:ManateeHistogram.png|400px|none]]
-[[Image:HistogramAll.png|400px|none]]
+[[Image:HistogramAll.png|600px|none]]
 These graphs show the frequency of gene lengths for the 3 different annotations. The x-axis ranges from 0 - 2,500 bps, with a step value of 50 bps. The Excel file used to generate these histograms can be downloaded by clicking [[Media:GeneLengths.xls|here]].

@@ Line 2: / Line 2: @@
 [[Image:RastHistogram.png|400px|none]]
 [[Image:ManateeHistogram.png|400px|none]]
+[[Image:HistogramAll.png|400px|none]]
 These graphs show the frequency of gene lengths for the 3 different annotations. The x-axis ranges from 0 - 2,500 bps, with a step value of 50 bps. The Excel file used to generate these histograms can be downloaded by clicking [[Media:GeneLengths.xls|here]].

@@ Line 6: / Line 6: @@
 Below are some descriptive statistics for the data shown above. From these statistics, it is clear that, in general, the gene calls made by Rast were longer than the calls made by JGI or Manatee (some statistical analysis could show this more clearly). This supports the claim that Rast called more alternative start codons, resulting in longer genes and different start indices (see [[Venn diagrams]]).
 {| border="1"
 |+ Gene Length Descriptive Statistics

← Older revision		Revision as of 18:19, 30 September 2008
Line 3:		Line 3:
	[[Image:RastHistogram.png\|400px\|none]]		[[Image:RastHistogram.png\|400px\|none]]
	[[Media:GeneLengths.xls]]		[[Media:GeneLengths.xls]]
		+
		+	{\| border="1"
		+	\|+ Gene Length Descriptive Statistics
		+	! Statistic !! JGI !! RAST !! Manatee
		+	\|-
		+	! Mean
		+	\| 869.9 \|\| 941.8 \|\| 844.9
		+	\|-
		+	! Median
		+	\| 728 \|\| 801.5 \|\| 692
		+	\|-
		+	! Mode
		+	\| 428 \|\| 284 \|\| 116
		+	\|-
		+	! Minimum
		+	\| 70 \|\| 70 \|\| 73
		+	\|-
		+	! Maximum
		+	\| 7130 \|\| 100001 \|\| 10001
		+	\|-
		+	! Count
		+	\| 3097 \|\| 2898 \|\| 3254
		+	\|}

@@ Line 1: / Line 1: @@
-[[Image:JGIHistogram.png|500px|none]]
+[[Image:JGIHistogram.png|400px|none]]
-[[Image:ManateeHistogram.png|500px|none]]
+[[Image:ManateeHistogram.png|400px|none]]
-[[Image:RastHistogram.png|500px|none]]
+[[Image:RastHistogram.png|400px|none]]