Personal tools

Template:F5samples: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 293: Line 293:
== 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