Personal tools

Template:F5samplesTest: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
mNo edit summary
mNo edit summary
Line 46: Line 46:
! Additional information
! Additional information
|-
|-
|<div id="css-table"><div class="col">Transcriptome profiling<table cellspacing="0" border="1">
|<div id="css-table"><div class="col">Sample information<table cellspacing="0" border="1">
<tr><th>[[Property:profile_hcage|hCAGE]]:</th><td>{{#switch: {{{profile_hcage}}}|,,,=NA| =NA |{{{profile_hcage}}}}}</td></tr>
<tr><th>[[Property:profile_rnaseq|RNA-seq]]:</th><td>{{#switch: {{{profile_rnaseq}}}|,,,=NA| =NA |{{{profile_rnaseq}}}}}</td></tr>
<tr><th>[[Property:profile_srnaseq|smallRNA seq]]:</th><td>{{#switch: {{{profile_srnaseq}}}|,,,=NA| =NA |{{{profile_srnaseq}}}}} </td></tr>
<tr><th>[[Property:profile_cagescan|nanoCAGEscan]]:</th><td>{{#switch: {{{profile_cagescan}}}|,,,=NA| =NA |{{{profile_cagescan}}}}}</td></tr>
</table></div><div class="col">Sample information<table cellspacing="0" border="1">
<tr><th>[[Property:sample_strain|strain]]: </th><td>{{#switch:{{{sample_strain}}}|,,,=NA| =NA |{{{sample_strain}}}}}</td></tr>
<tr><th>[[Property:sample_strain|strain]]: </th><td>{{#switch:{{{sample_strain}}}|,,,=NA| =NA |{{{sample_strain}}}}}</td></tr>
<tr><th>[[Property:sample_tissue|tissue]]:</th><td>{{#switch:{{{sample_tissue}}}|,,,=NA| =NA |{{{sample_tissue}}}}}</td></tr>
<tr><th>[[Property:sample_tissue|tissue]]:</th><td>{{#switch:{{{sample_tissue}}}|,,,=NA| =NA |{{{sample_tissue}}}}}</td></tr>
Line 70: Line 65:
<tr><th>[[Property:sample_note|Note]]:</th><td>{{#switch:{{{sample_note}}}|,,,=NA| =NA |{{{sample_note}}}}}</td></tr>
<tr><th>[[Property:sample_note|Note]]:</th><td>{{#switch:{{{sample_note}}}|,,,=NA| =NA |{{{sample_note}}}}}</td></tr>
{{#if:{{{sample_info_link}}}|<tr><th style="background-color: #4169e1;">External link for information</th><td style="background-color: #f0f8ff;">[{{#explode:{{{sample_info_link}}}|;|-1}} {{#explode:{{{sample_info_link}}}|;|0}}]</td></tr>}}</table></div>
{{#if:{{{sample_info_link}}}|<tr><th style="background-color: #4169e1;">External link for information</th><td style="background-color: #f0f8ff;">[{{#explode:{{{sample_info_link}}}|;|-1}} {{#explode:{{{sample_info_link}}}|;|0}}]</td></tr>}}</table></div>
<div class="col">RNA information<table cellspacing="0" border="1">
<div class="col">Transcriptome profiling<table cellspacing="0" border="1">
<tr><th>[[Property:profile_hcage|hCAGE]]:</th><td>{{#switch: {{{profile_hcage}}}|,,,=NA| =NA |{{{profile_hcage}}}}}</td></tr>
<tr><th>[[Property:profile_rnaseq|RNA-seq]]:</th><td>{{#switch: {{{profile_rnaseq}}}|,,,=NA| =NA |{{{profile_rnaseq}}}}}</td></tr>
<tr><th>[[Property:profile_srnaseq|smallRNA seq]]:</th><td>{{#switch: {{{profile_srnaseq}}}|,,,=NA| =NA |{{{profile_srnaseq}}}}} </td></tr>
<tr><th>[[Property:profile_cagescan|nanoCAGEscan]]:</th><td>{{#switch: {{{profile_cagescan}}}|,,,=NA| =NA |{{{profile_cagescan}}}}}</td></tr>
</table></div>
<div>RNA information<table cellspacing="0" border="1">
<tr><th>[[Property:sample_id|sample_id]]:</th><td>{{#switch:{{{sample_id}}}|,,,=NA| =NA |{{{sample_id}}}}}</td></tr>
<tr><th>[[Property:sample_id|sample_id]]:</th><td>{{#switch:{{{sample_id}}}|,,,=NA| =NA |{{{sample_id}}}}}</td></tr>
<tr><th>[[Property:rna_tube_id|tube_id]]:</th><td>{{#switch:{{{rna_tube_id}}}|,,,=NA| =NA |{{{rna_tube_id}}}}}</td></tr>
<tr><th>[[Property:rna_tube_id|tube_id]]:</th><td>{{#switch:{{{rna_tube_id}}}|,,,=NA| =NA |{{{rna_tube_id}}}}}</td></tr>

Revision as of 16:41, 7 April 2014

Name:{{{name}}}
Species:{{{sample_species}}}
Library ID:{{{library_id}}}
Sample type:{{{sample_category}}}
Genomic View:zenbu , UCSC
Additional information
Sample information
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}}}
company:{{{sample_company}}}
collaboration:{{{sample_collaboration}}}
Experimental condition:{{{sample_experimental_condition}}}
disease:{{{sample_disease}}}
cell_lot;{{{sample_cell_lot}}}
cell_catalog:{{{sample_cell_catalog}}}
donor(cell lot):{{{sample_donor(cell lot)}}}
company:{{{sample_company}}}
Note:{{{sample_note}}}
External link for information[{{{sample_info_link}}} {{{sample_info_link}}}]
Transcriptome profiling
hCAGE:{{{profile_hcage}}}
RNA-seq:{{{profile_rnaseq}}}
smallRNA seq:{{{profile_srnaseq}}}
nanoCAGEscan:{{{profile_cagescan}}}
RNA information
sample_id:{{{sample_id}}}
tube_id:{{{rna_tube_id}}}
box:{{{rna_box}}}
position:{{{rna_position}}}
tube_id:{{{rna_tube_id}}}
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}}}
weight_ug:{{{rna_weight_ug}}}
concentration:{{{rna_concentration}}}
extraction_protocol:(Details){{{rna_extraction_protocol}}}



Co-expression clusters with enriched expression in this sampleRanked list of co-expression cluster expression in this sample relative to the median expression in the FANTOM5 collection is shown. Value is log10 transformed. <br>Analyst:NA <br><br>link to dataset.<br>data
Repeat families with enriched expression in this sample<b>Summary:</b>Ranked list of repeat family expression in this sample relative tothe median expression in the FANTOM5 collection is shown. Value is log10transformed.<br><b>Analyst:</b>NA<br><br>link to dataset.<br>data

no result for this sample



TFBS(DNA)motifs over-represented in proximal region of promoters active in this sample


JASPAR motifs<b>Summary:</b>Association of JASPAR motif to the promoter expression in thissample. Pearson's correlation between the number of TFBSs estimated byusing the position-weight matrix for each promoter and its expression isexpressed as Z-score by taking the ones based on random position-weightmatrix, and the tail probability of the normal distribution correspondingto the Z-score is taken as the resulting P-value. Lower P-value indicatesmore (non-random) association of the motif to promoter expression<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data

library id: {{{profile_hcage}}}This sample isn't target for the analysis

FANTOM5 phase1 novel unique motifs<b>Summary:</b>Association of the 169 novel and unique motifs discovered in FANTOM5 phase1 in this sample. Among the de-novo motifs discovered by DMF, HOMER,ChIPMunk, and ScanAll, only novel motifs are selected after comparison with known motif sets, and their clustering based on MACRO-APE resulted in169 novel and unique motifs. Their association to the promoter expression is evaluated in the same way to the JASPAR motif above<br><b>Analyst:</b> Michiel de Hoon <br><br><br>link to dataset.<br>data
library id: {{{profile_hcage}}}This sample isn't target for the analysis



de novo motifs identified by HOMER in promoters active in this sample<b>Summary:</b>The result of HOMER in this sample is shown.<br><b>Analyst:</b>NA <br> library id: {{{profile_hcage}}}




FANTOM5 (FF) ontology


Direct parent terms

is_a relathionship
{{{is_a}}}

part_of relathionship
{{{part_of}}}

has_quality relathionship
{{{has_quality}}}

Ancestor terms (non development)<b>Summary:</b>Connected ontology terms with is_a, part_of or located_in relationship <br><b>Analyst:</b> Hideya Kawaji<br><br>link to source data<br>data

CL: Cell type
NA

DOID: Disease
NA

UBERON: Anatomy
NA

FF: FANTOM5
NA

Ancestor terms (development)<b>Summary:</b>Connected ontology terms with develops_from, derives_from or preceded_by relationship <br><b>Analyst:</b> Hideya Kawaji <br><br>link to source data<br>data
NA






















Property "Sample seq library id" (as page type) with input value "{{{profile_hcage}}}" contains invalid characters or is incomplete and therefore can cause unexpected results during a query or annotation process.