Personal tools

Test: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
mNo edit summary
No edit summary
 
(6 intermediate revisions by the same user not shown)
Line 1: Line 1:
{{f5samplesTest
 
|DRA_sample_Accession=chicken_CAGE@SAMD00053745
Data sources used in FANTOM5 SSTAR
|DRA_sample_Accession_Zoo=chicken_sRNA@SAMD00053745
 
|accession_numbers=chicken_CAGE;DRX057267;DRR063026;DRZ007521;DRZ007553
 
|accession_numbers_Zoo=chicken_sRNA;DRX163585;DRR172974;DRZ014421!chicken_sRNA;DRX163586;DRR172975;DRZ014422
=== CAGE peaks ===
|ancestors_in_anatomy_facet=UBERON:0000468,UBERON:0000922,UBERON:0000479,UBERON:0000061,UBERON:0000465,UBERON:0001062
* CAGE peak location (with the robust threshold) , annotation, and expression
|ancestors_in_cell_lineage_facet=
** <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>
|ancestors_in_disease_facet=
** <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>
|ancestors_in_ff_facet=FF:0000102,FF:0000101,FF:0000032,FF:0000001,FF:0000004,FF:0000649
* Ontology-based sample term enrichment analysis
|comment=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]</span>
|created_by=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Mouse]</span>
|creation_date=
 
|def=
=== Genes ===
|fonse_cell_line=
* Transcription factors (curated list)
|fonse_cell_line_closure=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_human_official.xls Human]</span>
|fonse_cellprecursor=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse]</span>
|fonse_cellprecursor_closure=
 
|fonse_developsfrom=
* Gene details (obtained from EntrezGene)
|fonse_developsfrom_closure=
** <span class="plainlinks">[ftp://ftp.ncbi.nih.gov/gene/DATA/ Human and Mouse]</span>
|fonse_disease=
 
|fonse_disease_closure=
=== Coexpression module ===
|fonse_isa=
* FFCP member list
|fonse_isa_closure=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/SYNC015_combined_clustertables.txt Human]</span>
|fonse_location=
** <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_location_closure=
* Sample ontology enrichment analysis
|fonse_organ=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]</span>
|fonse_organ_closure=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse]</span>
|fonse_organismsubdivision=
* GOStat results on Coexpression module
|fonse_organismsubdivision_closure=
** <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=
** <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_sampletype_closure=
* Pathway enrichment analysis
|fonse_stage=
** <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_stage_closure=
** <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=
* TFBS overrepresentation
|fonse_system_closure=
** <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=
** <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_taxon_closure=
** <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=
** <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>
|fonse_treatment_closure=
* <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>
|has_quality=
* Relative expression of the co-expression module
|id=FF:10004-101A9
** <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_a=FF:0000004;;FF:0000032;;FF:0000649;;UBERON:0000922
** <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>
|is_obsolete=
 
|library_id=CNhs10485
=== Motifs ===
|name=chicken embryo whole body, day10 (HH37)
* Novel motifs GREAT analysis results
|namespace=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]</span>
|part_of=
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse]</span>
|profile_cagescan=,,,
* Novel motifs Significance of the correlation with CAGE expression
|profile_hcage=CNhs10485,LSID656,release008,COMPLETED
** <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_rnaseq=,,,
** <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>
|profile_srnaseq=SRhi10006,,,
* Jaspar motifs Significance of the correlation with CAGE expression
|rna_box=101
** <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_catalog_number=NA
** <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_concentration=4.4
 
|rna_extraction_protocol=OP-RNA-extraction-totalRNA-TRIzol-isopropanol-v1.0
=== Sample ===
|rna_lot_number=NA
* sample name and attributes
|rna_od260/230=1.686666667
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/HumanSamples2.0.sdrf.xlsx Human]</span>
|rna_od260/280=1.943333333
** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/MouseSamples2.3.sdrf.xlsx Mouse]</span>
|rna_position=A9
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression]</span>
|rna_rin=9.9
* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs]</span>
|rna_sample_type=total RNA
* Repeat family, relative expression
|rna_tube_id=101A9
** <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>
|rna_weight_ug=800
** <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_age=
 
|sample_category=tissues
=== Ontology ===
|sample_cell_catalog=NA
* <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_line=
* <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_lot=NA
 
|sample_cell_type=CELL MIXTURE - tissue sample
=== CAGEd-oPOSSUM ===
|sample_collaboration=Guojun Sheng (RIKEN CDB)
* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/human/index.html Human]</span>
|sample_company=NA
* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/mouse/index.html Mouse]</span>
|sample_description=
|sample_dev_stage=10 days embryo
|sample_disease=normal
|sample_donor(cell lot)=1
|sample_ethnicity=
|sample_experimental_condition=
|sample_id=10004
|sample_note=
|sample_sex=unknown
|sample_species=Gallus gallus
|sample_strain=
|sample_tissue=whole body
|top_motifs=
|xref=
|zoo_library_id=SRhi10006.GGCTAC!SRhi10007.GGTAGC
|zenbu_report=https://fantom.gsc.riken.jp/zenbu/reports/#miRNA_expression_atlas_chicken;search_select_hide=table111:FF:10004-101A9;search_select_hide=table117:FF:10004-101A9
}}

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

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Test&oldid=4578777"