Template:F5samplesTest
From FANTOM5_SSTAR
| Name: | {{{name}}} |
|---|---|
| Species: | {{{sample_species}}} |
| Library ID: | {{{library_id}}} |
| Sample type: | {{{sample_category}}} |
| Genomic View: | zenbu , UCSC |
| Additional information | ||||||||||||||||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Sample information
RNA information
|
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}}}
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
