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Template:F5samples: Difference between revisions

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<br>{{#if: {{#pos:{{{profile_hcage}}}|CNhs}} |{{Fontsize|3|TF to Motif to TF network }}{{#info:Mouseover nodes and edges to see attributes.  Motifs are shown in orange, TFs are shown in blue.  Promoter and z-score are attributes of the Motif to TF edges (blue arrow).  TF to Motif edges are shown in orange.<br>Motifs shown are the top (maximum 30) motifs in the sample.  TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample.  Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).<br>Analyst: Erik Arner<br>Application Developer: Jayson HARSHBARGER}}
<br><br>{{#if: {{#pos:{{{profile_hcage}}}|CNhs}} |{{Fontsize|3|TF to Motif to TF network }}{{#info:Mouseover nodes and edges to see attributes.  Motifs are shown in orange, TFs are shown in blue.  Promoter and z-score are attributes of the Motif to TF edges (blue arrow).  TF to Motif edges are shown in orange.<br>Motifs shown are the top (maximum 30) motifs in the sample.  TFs shown have at least one CAGE promoter with at at least 10 TPM expression (RLE normalized) in the sample.  Edges shown have a z-score of at least 1.5 (based on correlation between motif activity and promoter expression).<br>Analyst: Erik Arner<br>Application Developer: Jayson HARSHBARGER}}
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
{{#arraymap:{{#explode:{{{profile_hcage}}}|,|0}}|&|$
|{{#outerfile_existance:/resource_browser/nwfiles/$.{{PAGENAME}}.xgmml|{{Tf_motif_cytoscapenw|CNhs=$|FFid={{PAGENAME}}}}
|{{#outerfile_existance:/resource_browser/nwfiles/$.{{PAGENAME}}.xgmml|{{Tf_motif_cytoscapenw|CNhs=$|FFid={{PAGENAME}}}}

Revision as of 15:32, 18 June 2014

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





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.