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<tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr>
<tr><th scope="row" align="right">Name:</th><td>[[name::{{{name}}}]]</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_species|Species]]:</th><td>[[sample_species::{{{sample_species}}}]]</td></tr>
<tr><th scope="row" align="right">[[Property:Library_accession_number|Library]]:</th><td>{{LibraryIds|{{{library_id_phase_based}}}}}</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_category|Sample type]]:</th><td>{{{sample_category}}}</td></tr>
<tr><th scope="row" align="right">[[Property:Sample_category|Sample type]]:</th><td>{{{sample_category}}}</td></tr>
<tr><th scope="row" align="right">Genomic View:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [https://fantom5-collaboration.gsc.riken.jp/ucsc/cgi-bin/hgTracks?db={{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | hg19 | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mm9 | }}{{#ifeq: {{{sample_species}}} | Rat (Rattus rattus) |  rn4 | }}{{#ifeq: {{{sample_species}}} | Dog (Canis lupus familaris) | canFam2 | }}{{#ifeq: {{{sample_species}}} | Chicken (Gallus gallus) | galGal3 | }}&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC] </td></tr></table>
<tr><th scope="row" align="right">Genomic View:</th><td>[https://fantom5-collaboration.gsc.riken.jp/zenbu/dex/#section=Experiments;search={{#replace:{{{id}}}|FF:|}} zenbu] , [https://fantom5-collaboration.gsc.riken.jp/ucsc/cgi-bin/hgTracks?db={{#ifeq: {{{sample_species}}} | Human (Homo sapiens) | hg19 | }}{{#ifeq: {{{sample_species}}} | Mouse (Mus musculus) | mm9 | }}{{#ifeq: {{{sample_species}}} | Rat (Rattus rattus) |  rn4 | }}{{#ifeq: {{{sample_species}}} | Dog (Canis lupus familaris) | canFam2 | }}{{#ifeq: {{{sample_species}}} | Chicken (Gallus gallus) | galGal3 | }}&tsCurTab=advancedTab&hgt_tsPage=&hgt_tSearch=search&tsName={{#replace:{{{id}}}|FF:|}} UCSC] </td></tr>
<tr><th scope="row" align="right">[[Property:Library_id|Library]]:</th><td>{{LibraryIds|{{{library_id_phase_based}}}}}</td></tr></table>
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto"
{|class="wikitable mw-collapsible mw-collapsed" style="width:auto"
! Additional information
! Additional information
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<br><br>
<br><br>
{{#arraydefine:libids_array|{{#arraymap:{{library_id_phase_based}}|;|$|{{#explode:$|:|1}}}}|,}}
{{#vardefine:libraryidsall|{{#arrayprint:libids_array|!}}}}
{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|
{{#if:{{#pos:{{{DRA_sample_Accession}}}|@|0}}|
{{#set:sample_category={{{sample_category}}}}}
{{#set:sample_category={{{sample_category}}}}}
{{#arraymap:{{{library_id}}}|!|$
{{#arraymap:{{#var:libraryidsall}}|!|$
|{{#set:Library accession number=$}}
|{{#set:Library id=$}}
}}
}}



Revision as of 14:36, 17 June 2014

Name:{{{name}}}
Species:{{{sample_species}}}
Sample type:{{{sample_category}}}
Genomic View:zenbu , UCSC
Library:
Library id:
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}}}
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}}}
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.