Personal tools

Data source: Difference between revisions

From FANTOM5_SSTAR

Jump to: navigation, search
No edit summary
No edit summary
Line 5: Line 5:
== old info on the top page ==
== old info on the top page ==
* CAGE peaks (only the robust set), their association with genes, and their expression based on RLE TPM.
* CAGE peaks (only the robust set), their association with genes, and their expression based on RLE TPM.
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz]
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz
** [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz]
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.osc.txt.gz
* Swissregulon motifs, and Motif Activity Response Analysis (MARA)
* Swissregulon motifs, and Motif Activity Response Analysis (MARA)
** [http://www.swissregulon.unibas.ch/
** http://www.swissregulon.unibas.ch/
https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/MotifActivity/[
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/mdehoon/MotifActivity/
* FF Ontology
* FF Ontology
**[https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FANTOM5v5/]
** https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FANTOM5v5/
* facet classification based on FF ontology
* facet classification based on FF ontology
** [http://yuri.lbl.gov:8600/fonse/ FONSE (Fantomy ONtology Sample Explorer)]
** http://yuri.lbl.gov:8600/fonse/ FONSE (Fantomy ONtology Sample Explorer)




Line 20: Line 20:
=== CAGE peaks ===
=== CAGE peaks ===
* CAGE peak location (with the robust threshold) , annotation, and expression
* CAGE peak location (with the robust threshold) , annotation, and expression
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/description120126/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.desc.osc.txt.gz
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/description120126/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.desc.osc.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/description120126/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.desc.osc.txt.gz</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/description120126/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.tpm.selected.clustername_update.desc.osc.txt.gz
* Ontology-based sample term enrichment analysis
* Ontology-based sample term enrichment analysis
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment/
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment/
<!-- ** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v019_01_ontology_term_enrichment_1st/ --></pre>
<!-- ** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v019_01_ontology_term_enrichment_1st/ -->


=== Co expression cluster ===
=== Co expression cluster ===
* CP member list
* CP member list
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/FFCP_member_list/SYNC015_combined_clustertables.txt</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/FFCP_member_list/SYNC015_combined_clustertables.txt
* Sample ontology enrichment analysis
* Sample ontology enrichment analysis
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment_on_MCL_coexp_cluster_120516/</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v6_ontology_term_enrichment_on_MCL_coexp_cluster_120516/
* GOstat analysis
* GOstat analysis
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/gostat_analysis/go_all<pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/gostat_analysis/go_all
* KEGG enrichment
* KEGG enrichment
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/KEGG_pathway_enrichment_analysis/KEGG_enrichment.xlsx</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/co_expression_cluster/KEGG_pathway_enrichment_analysis/KEGG_enrichment.xlsx


=== Gene ===
=== Gene ===
* EntrezGene
* EntrezGene
<pre>https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
** https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz
https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz</pre>
** https://fantom5-collaboration.gsc.riken.jp/files/data/shared/external/entrez_gene/2012-01-19/DATA/GENE_INFO/Mammalia/Mus_musculus.gene_info.gz
* Transcription factors
* Transcription factors
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_May10.osc.txt.gz
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_May10.osc.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_enrichment_may10.txt.gz
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_enrichment_may10.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_May10.osc.txt.gz
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_May10.osc.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_enrichment_may10.txt.gz</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_enrichment_may10.txt.gz


=== Motifs ===
=== Motifs ===
* SwissRegulon (known)
* SwissRegulon (known)
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Swissregulon</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Motif/Swissregulon


=== Sample information ===
=== Sample information ===
* sample name and attributes
* sample name and attributes
<pre>https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:Helicos_data_production_schedule_June_25_2012.xls</pre>
** https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/File:Helicos_data_production_schedule_June_25_2012.xls
* GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples
* GOstat analysis based on ranked expression for human libraries in phase 1 freeze samples
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Samples/sample_rank_go</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Samples/sample_rank_go
* TF expression and enrichment table on FF sample page
* TF expression and enrichment table on FF sample page
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_May10.osc.txt.gz
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_May10.osc.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_enrichment_may10.txt.gz
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_human_enrichment_may10.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_May10.osc.txt.gz
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_May10.osc.txt.gz
https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_enrichment_may10.txt.gz</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/m.lizio/Robust_cluster_to_TF_20120321/TF2CLUSTER_mouse_enrichment_may10.txt.gz


=== Ontology ===
=== Ontology ===
* Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)
* Sample ontology(FF), Cell ontology(CL), Human disease ontology(DOID) and Uber anatomy ontology (UBERON)
<pre>https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FF_ontology_v019_01/</pre>
** https://fantom5-collaboration.gsc.riken.jp/files/data/shared/contrib/sample_ontology/FF_ontology_v019_01/
* Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term
* Ontology mapping: FF sample <--> CL, DOID, UBERON, FF term
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v019_01/</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/120322-FFontology/v019_01/


=== Network ===
=== Network ===
* MARA netwrok
* MARA netwrok
<pre>https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Network/mara_network</pre>
** https://fantom5-collaboration.gsc.riken.jp/webdav/home/shimoji/ResourceBrowser_data/Network/mara_network


= FANTOM5 BioMart =
= FANTOM5 BioMart =
Line 76: Line 76:


* CAGE peak location (with the permissive threshold) and its association with genes
* CAGE peak location (with the permissive threshold) and its association with genes
<pre>hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz
mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz</pre>
** mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update.bed.gz


* CAGE peak location (with the robust threshold) and its association with genes
* CAGE peak location (with the robust threshold) and its association with genes
<pre>hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.clustername_update.bed.gz
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.clustername_update.bed.gz
mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.clustername_update.bed.gz</pre>
** mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/tc.decompose_smoothing_merged.ctssMaxCounts11_ctssMaxTpm1.clustername_update.bed.gz


* CAGE peak descriptions
* CAGE peak descriptions
**hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/description120126/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update__description.txt.gz]
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/hg19/description120126/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update__description.txt.gz
**mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/description120126/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update__description.txt.gz]
** mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/kawaji/111220-DPI/mm9/description120126/tc.decompose_smoothing_merged.ctssMaxCounts3.clustername_update__description.txt.gz


* CpG island and TATA-box annotation
* CpG island and TATA-box annotation
**hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_hg19_20120116.permissive_set.TATA_CpG_annotated.osc.gz]
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_hg19_20120116.permissive_set.TATA_CpG_annotated.osc.gz
** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_mm9_20120116.full_set.TATA_CpG_annotated.osc.gz]
** mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/nbertin/CAGE-Tag-Cluster-Annotation_Jan12/DPIcluster_mm9_20120116.full_set.TATA_CpG_annotated.osc.gz


* Machine learning classification as TSS-like or not (KAUST)
* Machine learning classification as TSS-like or not (KAUST)
** hg19: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/FREEZE_PHASE1/cluster_classify/tc.decompose_smoothing_merged.permissive_peaks_pos.bed.gz]
** hg19: https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/FREEZE_PHASE1/cluster_classify/tc.decompose_smoothing_merged.permissive_peaks_pos.bed.gz
** mm9: [https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/FREEZE_PHASE1/cluster_classify/mm9.permissive_dpi_cluster.pos.bed.gz]
** mm9: https://fantom5-collaboration.gsc.riken.jp/webdav/home/seb/FREEZE_PHASE1/cluster_classify/mm9.permissive_dpi_cluster.pos.bed.gz


* T. Lassmann tss-like classifier (score):
* T. Lassmann tss-like classifier (score):

Revision as of 14:06, 15 August 2012

Data sources used in the database(s)


old info on the top page


FANTOM5 Resource Browser

CAGE peaks

Co expression cluster

Gene

Motifs

Sample information

Ontology

Network

FANTOM5 BioMart

CAGE peak annotation

CAGE peak expression (for the ones with the robust threshold)

Retrieved from "http://f5-webapp4.gsc.riken.jp/resource_browser/index.php?title=Data_source&oldid=2129078"