Data source: Difference between revisions

Latest revision as of 09:44, 17 February 2022

Data sources used in FANTOM5 SSTAR

CAGE peaks

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

Genes

Transcription factors (curated list)
- Human
- Mouse

Gene details (obtained from EntrezGene)
- Human and Mouse

Coexpression module

FFCP member list
- Human
- Mouse
Sample ontology enrichment analysis
- human
- mouse
GOStat results on Coexpression module
- human
- mouse
Pathway enrichment analysis
- human
- mouse
TFBS overrepresentation
ENCODE_TF_ChIP-seq_peak enrichment analysis
Relative expression of the co-expression module
- human
- mouse

Motifs

Novel motifs GREAT analysis results
- Human
- Mouse
Novel motifs Significance of the correlation with CAGE expression
- Human
- Mouse
Jaspar motifs Significance of the correlation with CAGE expression
- Human
- Mouse

Sample

sample name and attributes
- Human
- Mouse
Transcription factors, relative expression
HOMER motifs
Repeat family, relative expression
- human
- mouse

Ontology

CAGEd-oPOSSUM

Human
Mouse

@@ Line 1: / Line 1: @@
-Data sources used in the database(s)
+Data sources used in FANTOM5 SSTAR
-= FANTOM5 Resource Browser =
 === CAGE peaks ===
-* CAGE peak location (with the robust threshold) and its annotation
+* CAGE peak location (with the robust threshold) , annotation, and expression
-** https:://...
+** <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>
+** <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>
+* Ontology-based sample term enrichment analysis
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Human]</span>
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_CAGE_peaks/ Mouse]</span>
-* CAGE peak expression
+=== Genes ===
-** https:://...
+* Transcription factors (curated list)
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_human_official.xls Human]</span>
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/TF2CLUSTER_mouse_official.xls Mouse]</span>
-* Co expression cluster
+* Gene details (obtained from EntrezGene)
-** https:://...
+** <span class="plainlinks">[ftp://ftp.ncbi.nih.gov/gene/DATA/ Human and Mouse]</span>
-* GO enrichment analysis
+=== Coexpression module ===
-** https:://...
+* FFCP member list
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/SYNC015_combined_clustertables.txt Human]</span>
+** <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>
+* Sample ontology enrichment analysis
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ human]</span>
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Sample_ontology_enrichment_of_coexpression_clusters/ mouse]</span>
+* GOStat results on Coexpression module
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_GOstats.tar.gz human]</span>
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_GOstats.tar.gz mouse]</span>
+* Pathway enrichment analysis
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/hg19_co-expression_modules.tar.gz human]</span>
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Co-expression_clusters/mm9_co-expression_modules.tar.gz mouse]</span>
+* TFBS overrepresentation
+** <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>
+** <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>
+** <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>
+** <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>
+* <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>
+* Relative expression of the co-expression module
+** <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>
+** <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>
-* Sample enrichment analysis
+=== Motifs ===
-** https:://...
+* Novel motifs GREAT analysis results
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/hg19.table.txt Human]</span>
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/novel_GREAT_analysis_results/mm9.table.txt Mouse]</span>
+* Novel motifs Significance of the correlation with CAGE expression
+** <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>
+** <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>
+* Jaspar motifs Significance of the correlation with CAGE expression
+** <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>
+** <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>
-=== Gene ===
+=== Sample ===
+* sample name and attributes
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/HumanSamples2.0.sdrf.xlsx Human]</span>
+** <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.6/basic/MouseSamples2.3.sdrf.xlsx Mouse]</span>
+* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Transcription_factors/ Transcription factors, relative expression]</span>
+* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase1.1/extra/Motifs/ HOMER motifs]</span>
+* Repeat family, relative expression
+** <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>
+** <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>
-* EntrezGene
+=== Ontology ===
-** https:://...
+* <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>
+* <span class="plainlinks">[https://fantom.gsc.riken.jp/5/datafiles/phase2.0/extra/Ontology/ Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term]</span>
-* Transcription factors
+=== CAGEd-oPOSSUM ===
-** https:://...
+* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/human/index.html Human]</span>
+* <span class="plainlinks">[https://cagedop.cmmt.ubc.ca/CAGEd_oPOSSUM/results/precomputed/mouse/index.html Mouse]</span>
-=== motifs ===
-* SwissRegulon
-** https:://...
-* de novo motifs (HOMER)
-** https:://...
-=== Sample classification ===
-* sample name
-** phase1 freeze https:://...
-* sample attributes
-** Marina's excel?  https:://...
-* sample ontology
-** FF ontology v6 https:://...
-= FANTOM5 BioMart =
-=== CAGE peak annotation (for the ones with the permissive threshold) ===
-* CAGE peak location (with the permissive threshold) and its association with genes
-** https:://...
-* CpG island and TATA-box annotation
-** https:://...
-* Machine learning classification as TATA-like or not (KAUST)
-** https:://...
-=== CAGE peak expression (for the ones with the robust threshold) ===
-* Counts
-** https:://...
-* TPM (RLE normalization-based)
-** https:://...
-* Relative expression
-** https:://...

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From FANTOM5_SSTAR

Latest revision as of 09:44, 17 February 2022

Contents

CAGE peaks

Genes

Coexpression module

Motifs

Sample

Ontology

CAGEd-oPOSSUM

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