Template:F5samples: Difference between revisions
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== Repeat Enrichment == | == Repeat Enrichment == | ||
{{#info: <br>Analyst: }} | {{#info: <br>Analyst: }} | ||
{{#if: {{#pos:{{{repeat_enrich_byfamily}}}|,}} | | |||
=== Categorized by Family === | |||
<html> | |||
<script type="text/javascript"> | |||
$(document).ready(function() { | |||
var repeat_enrich_byfamily_data = []; | |||
var repeat_enrich_byfamily_repnames = ['Alu','Alu,Alu','Alu,ERVL-MaLR','Alu,L1','Alu,L2','Alu,Low_complexity','Alu,MIR','Alu,hAT-Charlie','Alu,hAT-Tip100','Alu,rRNA','Alu,snRNA','CR1','CR1,CR1','DNA','DNA?','Deu','ERV','ERV1','ERV1,ERV1','ERV1,ERVL','ERV1,ERVL-MaLR','ERV1,MIR','ERV1,snRNA','ERVK','ERVK,rRNA','ERVL','ERVL,ERV1','ERVL,ERVL','ERVL,ERVL-MaLR','ERVL,hAT-Charlie','ERVL,snRNA','ERVL-MaLR','ERVL-MaLR,ERVL-MaLR','ERVL-MaLR,snRNA','ERVL?','Gypsy','Gypsy?','Helitron','L1','L1,ERV1','L1,ERVL','L1,ERVL-MaLR','L1,L1','L1,TcMar-Mariner','L1,TcMar-Tigger','L1,hAT-Charlie','L1,rRNA','L1,snRNA','L1?','L2','L2,ERV1','L2,ERVL-MaLR','L2,L2','L2,MIR','L2,hAT-Blackjack','L2,hAT-Charlie','LTR','Low_complexity','Low_complexity,Alu','Low_complexity,ERV1','Low_complexity,L2','Low_complexity,Low_complexity','Low_complexity,Low_complexity,Low_complexity','Low_complexity,snRNA','MIR','MIR,ERVL-MaLR','MIR,Low_complexity','MIR,MIR','Merlin','MuDR','NA','Other','PiggyBac','PiggyBac?','RNA','RNA,MIR','RTE','RTE,CR1','RTE-BovB','SINE','SINE?','Satellite','Satellite,ERVL','Simple_repeat','Simple_repeat,Alu','Simple_repeat,ERV1','Simple_repeat,ERVL','Simple_repeat,ERVL-MaLR','Simple_repeat,L1','Simple_repeat,L2','Simple_repeat,Low_complexity','Simple_repeat,Low_complexity,Low_complexity','Simple_repeat,MIR','Simple_repeat,Other','Simple_repeat,Simple_repeat','Simple_repeat,Simple_repeat,Low_complexity','Simple_repeat,Simple_repeat,Simple_repeat','Simple_repeat,TcMar-Tigger','Simple_repeat,Unknown','Simple_repeat,hAT-Charlie','Simple_repeat,hAT-Tip100','Simple_repeat,scRNA','Simple_repeat,snRNA','TcMar','TcMar-Mariner','TcMar-Tc2','TcMar-Tc2,ERV1','TcMar-Tigger','TcMar-Tigger,TcMar-Tigger','TcMar-Tigger,snRNA','TcMar?','Unknown','Unknown?','acro','centr','hAT','hAT-Blackjack','hAT-Charlie','hAT-Charlie,ERVL-MaLR','hAT-Charlie,MIR','hAT-Charlie,hAT-Charlie','hAT-Charlie,snRNA','hAT-Tip100','hAT?','rRNA','rRNA,rRNA','scRNA','scRNA,L1','snRNA','srpRNA','tRNA','telo']; | |||
var repeat_enrich_byfamily_values = [</html>{{{repeat_enrich_byfamily}}}<html>]; | |||
for(i1=0;i1<repeat_enrich_byfamily_repnames.length;i1++){ | |||
repeat_enrich_byfamily_data.push([repeat_enrich_byfamily_repnames[i1],repeat_enrich_byfamily_values[i1]]); | |||
} | |||
$('#repeat_enrich_byfamily_table').dataTable({ | |||
"sScrollY": "300px", | |||
"bScrollCollapse": true, | |||
"bPaginate": false, | |||
"bFilter": false, | |||
"bInfo": false, | |||
"aaData": repeat_enrich_byfamily_data, | |||
"aoColumns": [{ "sTitle": "Repeat sequence name", "bSortable": false },{ "sTitle": "Enrichment score", "sType": "numeric" }], | |||
"aaSorting": [[ 1, "desc" ]] | |||
}); | |||
}); | |||
</script> | |||
<table id="repeat_enrich_byfamily_table"></table> | |||
</html> | |||
|no result for this sample | |||
}} | |||
<!-- | |||
{{#if: {{#pos:{{{repeat_enrich_byname}}}|,}} | | {{#if: {{#pos:{{{repeat_enrich_byname}}}|,}} | | ||
<html> | <html> | ||
Line 322: | Line 352: | ||
|no result for this sample | |no result for this sample | ||
}} | }} | ||
--> | |||
== Relative expression of the co-expression cluster == | == Relative expression of the co-expression cluster == |
Revision as of 13:03, 21 September 2012
Name: | {{{name}}} |
---|---|
Species: | {{{sample_species}}} |
Genomic View: | zenbu , UCSC |
Details
Transcriptome profiling
hCAGE | {{{profile_hcage}}} |
---|---|
RNA-seq | {{{profile_rnaseq}}} |
smallRNA seq | {{{profile_srnaseq}}} |
nanoCAGEscan | {{{profile_cagescan}}} |
Sample info
strain | {{{sample_strain}}} |
---|---|
tissue | {{{sample_tissue}}} |
dev_stage | {{{sample_dev_stage}}} |
sex | {{{sample_sex}}} |
age | {{{sample_age}}} |
ethnicity | {{{sample_ethnicity}}} |
cell_type | {{{sample_cell_type}}} |
cell_line | {{{sample_cell_line}}} |
collaboration | {{{sample_collaboration}}} |
Experimental condition | {{{sample_experimental_condition}}} |
disease | {{{sample_disease}}} |
cell_lot | {{{sample_cell_lot}}} |
cell_catalog | {{{sample_cell_catalog}}} |
company | {{{sample_company}}} |
donor(cell lot) | {{{sample_donor(cell lot)}}} |
Note | {{{sample_note}}} |
RNA info
sample_id | {{{sample_id}}} |
---|---|
tube_id | {{{rna_tube_id}}} |
box | {{{rna_box}}} |
position | {{{rna_position}}} |
lot_number | {{{rna_lot_number}}} |
catalog_number | {{{rna_catalog_number}}} |
RIN | {{{rna_rin}}} |
OD260/230 | {{{rna_od260/230}}} |
OD260/280 | {{{rna_od260/280}}} |
sample_type | {{{rna_sample_type}}} |
extraction_protocol | {{{rna_extraction_protocol}}} |
weight_ug | {{{rna_weight_ug}}} |
concentration | {{{rna_concentration}}} |
Parent ontology
is_a relathionship
{{{is_a}}}
part_of relathionship
{{{part_of}}}
has_quality relathionship
{{{has_quality}}}
Ancestors in ontology (non-development)
Connected ontology terms with is_a, part_of or located_in relathionship <br>Analyst: Hideya Kawaji
CL: Cell type
DOID: Disease
Property "Ancestors in disease facet" (as page type) with input value "{{{ancestors_in_disease_facet}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.
UBERON: Anatomy
FF: FANTOM5
Ancestors in ontology (development)
Connected ontology terms with develops_from, derives_from or preceded_by relathionship <br>Analyst: Hideya Kawaji
Related MacroAPE_1083 Motifs
The values shown are the p-values of the motif in FANTOM5 samples. <br>Analyst: Michiel de Hoon This sample isn't target for the analysis
Repeat Enrichment
<br>Analyst:
no result for this sample
Relative expression of the co-expression cluster
<br>Analyst:
No results for this sample