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{{f5samplesTest
 
|DRA_sample_Accession=chicken_CAGE@SAMD00053773
Data sources used in FANTOM5 SSTAR
|accession_numbers=chicken_CAGE;DRX057269;DRR063028;DRZ007523;DRZ007555
 
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0001135,UBERON:0000947,UBERON:0001637,UBERON:0000483,UBERON:0000479,UBERON:0000055,UBERON:0004111,UBERON:0004120,UBERON:0000061,UBERON:0000465,UBERON:0003914,UBERON:0000025,UBERON:0000477,UBERON:0000467,UBERON:0001062,UBERON:0000480,UBERON:0000119,UBERON:0004573,UBERON:0002385,UBERON:0003509,UBERON:0007500,UBERON:0001981,UBERON:0004237,UBERON:0004695,UBERON:0002049,UBERON:0010317,UBERON:0002111,UBERON:0007798,UBERON:0001015,UBERON:0004178,UBERON:0002204,UBERON:0004535,UBERON:0004571,UBERON:0010191,UBERON:0000383,UBERON:0004572,UBERON:0004537,UBERON:0001009
 
|ancestors_in_cell_lineage_facet=CL:0000000,CL:0000003,CL:0000548,CL:0002371,CL:0000393,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000255,CL:0000359,CL:0002539
=== CAGE peaks ===
|ancestors_in_disease_facet=
* CAGE peak location (with the robust threshold) , annotation, and expression
|ancestors_in_ff_facet=FF:0000102,FF:0000002,FF:0000101,FF:0000032,FF:0000001,FF:0000033
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/hg19.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Human]</span>
|comment=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/CAGE_peaks/mm9.cage_peak_phase1and2combined_tpm_ann.osc.txt.gz Mouse]</span>
|created_by=
* Ontology-based sample term enrichment analysis
|creation_date=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]</span>
|def=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Mouse]</span>
|ffid_belonging_in_development=CL:0000355,CL:0000222,CL:0000514
 
|fonse_cell_line=
=== Genes ===
|fonse_cell_line_closure=
* Transcription factors (curated list)
|fonse_cellprecursor=CL:0000514
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_human_official.xls Human]</span>
|fonse_cellprecursor_closure=CL:0000003,CL:0000004,CL:0000012,CL:0000034,CL:0000048,CL:0000055,CL:0000056,CL:0000144,CL:0000220,CL:0000222,CL:0000255,CL:0000355,CL:0000514,CL:0000548,CL:0000680,CL:0000723,CL:0002321,CL:0002371
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse]</span>
|fonse_developsfrom=
 
|fonse_developsfrom_closure=
* Gene details (obtained from EntrezGene)
|fonse_disease=
** <span class="plainlinks">[ftp://ftp.ncbi.nih.gov/gene/DATA/ Human and Mouse]</span>
|fonse_disease_closure=
 
|fonse_isa=EFO:0002091,FF:0000033
=== Coexpression module ===
|fonse_isa_closure=CL:0000000,CL:0000003,CL:0000004,CL:0000012,CL:0000144,CL:0000183,CL:0000187,CL:0000192,CL:0000211,CL:0000255,CL:0000359,CL:0000393,CL:0000548,CL:0002371,CL:0002539,EFO:0000001,EFO:0000683,EFO:0002091,FF:0000001,FF:0000002,FF:0000032,FF:0000033,FF:0000101,FF:0000102,FF:11298-117B2,snap:Role,snap:SpecificallyDependentContinuant
* FFCP member list
|fonse_location=UBERON:0004178
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/SYNC015_combined_clustertables.txt Human]</span>
|fonse_location_closure=UBERON:0000025,UBERON:0000055,UBERON:0000061,UBERON:0000119,UBERON:0000383,UBERON:0000465,UBERON:0000467,UBERON:0000468,UBERON:0000477,UBERON:0000479,UBERON:0000480,UBERON:0000483,UBERON:0000947,UBERON:0001009,UBERON:0001015,UBERON:0001062,UBERON:0001135,UBERON:0001637,UBERON:0001981,UBERON:0002049,UBERON:0002111,UBERON:0002204,UBERON:0002385,UBERON:0003509,UBERON:0003914,UBERON:0004111,UBERON:0004120,UBERON:0004178,UBERON:0004237,UBERON:0004535,UBERON:0004537,UBERON:0004571,UBERON:0004572,UBERON:0004573,UBERON:0004695,UBERON:0007500,UBERON:0007798
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mouse_filtered2_p75_m22_T.clusters.txt Mouse]</span>
|fonse_organ=
* Sample ontology enrichment analysis
|fonse_organ_closure=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]</span>
|fonse_organismsubdivision=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse]</span>
|fonse_organismsubdivision_closure=
* GOStat results on Coexpression module
|fonse_sampletype=FF:0000002
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz human]</span>
|fonse_sampletype_closure=FF:0000002
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz mouse]</span>
|fonse_stage=
* Pathway enrichment analysis
|fonse_stage_closure=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz human]</span>
|fonse_system=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz mouse]</span>
|fonse_system_closure=UBERON:0000383,UBERON:0001009,UBERON:0002204,UBERON:0004535,UBERON:0004571,UBERON:0004572,UBERON:0007798
* TFBS overrepresentation
|fonse_taxon=FF:0000032
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.novel_motif.coexpression_clusters_overrepresentation.txt.gz human_novel_motif]</span>
|fonse_taxon_closure=FF:0000032
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz human_jaspar_motif]</span>
|fonse_treatment=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.novel_motif.coexpression_clusters_overrepresentation.txt.gz mouse_novel_motif]</span>
|fonse_treatment_closure=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9.KNOWN_JASPAR_130.coexpression_clusters_overrepresentation.txt.gz  mouse_jaspar_motif]</span>
|has_quality=
* <span class="plainlinks">[http://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/ENCODE_TF_ChIP-seq_peak_enrichment_coexprclusterencode.filtered.csv.gz ENCODE_TF_ChIP-seq_peak enrichment analysis]</span>
|id=FF:11298-117B2
* Relative expression of the co-expression module
|is_a=EFO:0002091;;FF:0000033
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_human_Aug3_2012.txt.gz human]</span>
|is_obsolete=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/coexpression_DPI_cluster_scores_median_mouse_Oct9_2012.txt.gz mouse]</span>
|library_id=CNhs11296
 
|name=Chicken Aortic Smooth Muscle cells, donor1
=== Motifs ===
|namespace=FANTOM5
* Novel motifs GREAT analysis results
|part_of=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]</span>
|profile_cagescan=,,,
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse]</span>
|profile_hcage=CNhs11296,LSID905,release009,COMPLETED
* Novel motifs Significance of the correlation with CAGE expression
|profile_rnaseq=,,,
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]</span>
|profile_srnaseq=SRhi10007,,,
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]</span>
|rna_box=117
* Jaspar motifs Significance of the correlation with CAGE expression
|rna_catalog_number=N/A
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/hg19.pvalues.txt Human]</span>
|rna_concentration=1.628
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/jaspar_Significance_of_the_correlation_with_CAGE_expression/mm9.pvalues.txt Mouse]</span>
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-miRNeasy_Mini-v1.0
 
|rna_lot_number=
=== Sample ===
|rna_od260/230=1.79
* sample name and attributes
|rna_od260/280=2.11
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/HumanSamples2.0.sdrf.xlsx Human]</span>
|rna_position=B2
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/MouseSamples2.3.sdrf.xlsx Mouse]</span>
|rna_rin=
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression]</span>
|rna_sample_type=total RNA
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs]</span>
|rna_tube_id=117B2
* Repeat family, relative expression
|rna_weight_ug=73.3
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_human_median_by_repFamilies_Aug06_2012.txt.gz human]</span>
|sample_age=U
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Repeat_expression/DPI_cluster_scores_mouse_median_by_repFamilies_Aug06_2012.txt.gz mouse]</span>
|sample_category=primary cells
 
|sample_cell_catalog=CAC35405
=== Ontology ===
|sample_cell_line=
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)]</span>
|sample_cell_lot=lot:2635
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term]</span>
|sample_cell_type=smooth muscle cell
 
|sample_collaboration=FANTOM5 OSC CORE (contact: Al Forrest)
=== CAGEd-oPOSSUM ===
|sample_company=Cell Applications
* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/human/index.html Human]</span>
|sample_description=
* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/mouse/index.html Mouse]</span>
|sample_dev_stage=
|sample_disease=
|sample_donor(cell lot)=
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=11298
|sample_note=
|sample_sex=unknown
|sample_species=Gallus gallus
|sample_strain=
|sample_tissue=aorta
|top_motifs=
|xref=
}}

Latest revision as of 20:55, 16 February 2022

Data sources used in FANTOM5 SSTAR


CAGE peaks

  • CAGE peak location (with the robust threshold) , annotation, and expression
  • Ontology-based sample term enrichment analysis

Genes

Coexpression module

Motifs

  • Novel motifs GREAT analysis results
  • Novel motifs Significance of the correlation with CAGE expression
  • Jaspar motifs Significance of the correlation with CAGE expression

Sample

Ontology

CAGEd-oPOSSUM