Time-courses resources: Difference between revisions

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== Links to data ==
== Links to data ==

=== List of time-course ===
*list of the time-courses in text format


=== Expression table 1 ===
=== Expression table 1 ===
*expression
*expression
* time-points with poor QC removed (Erik Arner's QC)
*RPM normalized
*RLE normalized
*for each tag cluster (TC)
*for each tag cluster (TC)
*for all time courses (phase 2)
*for all time courses (phase 2)


*https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/time_course_main_paper_freeze_feb2013/robust_dpi_expression/tc_expr.human.annot.csv.gz
(put link here)
*https://fantom5-collaboration.gsc.riken.jp/webdav/home/arner/timecourse/time_course_main_paper_freeze_feb2013/robust_dpi_expression/tc_expr.mouse.annot.csv.gz


=== Expression table 2 ===
=== Expression table 2 ===
*expression
*expression
*time-points with poor QC removed (Erik Arner's QC)
*RPM normalized
*RLE normalized
*for each tag cluster (TC)
*for each tag cluster (TC)
*for all snap-shots (phase 1) AND time courses (phase 2)
*for all snap-shots (phase 1) AND time courses (phase 2)
Line 19: Line 25:
=== TF expression table 2 ===
=== TF expression table 2 ===
*expression
*expression
*time-points with poor QC removed (Erik Arner's QC)
*RPM normalized
*RLE normalized
*for each tag cluster (TC)
*for each tag cluster (TC)
*for all snap-shots (phase 1) AND time courses (phase 2) - what makes most sense???
*for all snap-shots (phase 1) AND time courses (phase 2) - what makes most sense???
Line 27: Line 34:
=== Enhancer expression table ===
=== Enhancer expression table ===
*expression
*expression
*time-points with poor QC removed (Erik Arner's QC)
*RPM normalized
*matrices with raw counts as well as TPM and RLE normalized
*for each tag cluster (TC)
*based on [https://fantom5-collaboration.gsc.riken.jp/wiki/index.php/Enhancers#Enhancers_2 enhancers] identified using phase 1 and phase 2 non-filtered DPI tag clusters
*for all snap-shots (phase 1) AND time courses (phase 2)
*for all human and mouse snapshot and time course samples (UPDATE_022) with non-zero RLE factors (1827 human and 1036 mouse libraries)


[[Enhancers#Data]]
(put link here)


== Links to gene tables ==
== Links to gene tables ==
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*extract from individual time-course pages
*extract from individual time-course pages
*will be used to check each of the time-courses
*will be used to check each of the time-courses

=== List of early response marker genes ===

*Version 1.0 - Please see the README file for details, and send any feedback to [mailto:finn.drablos@ntnu.no Finn Drablos].
*''Potential'' immediate and early response (IER) genes extracted from literature.
**The README file - [[File:README_IER_genes_1.0.txt]]
**The list of potential IER genes - [[File:Potential_IER_genes_1.0.xls]]
**The source data (publications) - [[File:Source_data_IER_1.0.xls]]
**Visualization of overlap between list and F5 time course data (Erik Arner) [[File:Ier_updown.pdf]]


=== List of transcription factors ===
=== List of transcription factors ===
*link to existing list
*link to existing list

=== List of genes involved in epigenetics ===

*Version 1.0 - Please see the README file for details, and send any feedback to [mailto:finn.drablos@ntnu.no Finn Drablos].
**The README file - [[File:README_EpiGenesDB.txt]]
**The main gene list - [[File:EpiGenes_main_1.0.txt]]
**The histone genes - [[File:EpiGenes_histones_1.0.txt]]
**Genes considered, but not included - [[File:EpiGenes_removed_1.0.txt]]

*Version 1.1 - Added mouse orthologs to the lists of human genes. Now stored in Excel format.
**The README file - [[File:README_EpiGenesDB_1.1.txt]]
**The main gene list - [[File:EpiGenes_main_1.1.xls]]
**The histone genes - [[File:EpiGenes_histones_1.1.xls]]
**Genes considered, but not included - [[File:EpiGenes_removed_1.1.xls]]

Latest revision as of 15:21, 5 April 2013

Links to data

List of time-course

  • list of the time-courses in text format

Expression table 1

  • expression
  • time-points with poor QC removed (Erik Arner's QC)
  • RLE normalized
  • for each tag cluster (TC)
  • for all time courses (phase 2)

Expression table 2

  • expression
  • time-points with poor QC removed (Erik Arner's QC)
  • RLE normalized
  • for each tag cluster (TC)
  • for all snap-shots (phase 1) AND time courses (phase 2)

(put link here)

TF expression table 2

  • expression
  • time-points with poor QC removed (Erik Arner's QC)
  • RLE normalized
  • for each tag cluster (TC)
  • for all snap-shots (phase 1) AND time courses (phase 2) - what makes most sense???

(put link here)

Enhancer expression table

  • expression
  • time-points with poor QC removed (Erik Arner's QC)
  • matrices with raw counts as well as TPM and RLE normalized
  • based on enhancers identified using phase 1 and phase 2 non-filtered DPI tag clusters
  • for all human and mouse snapshot and time course samples (UPDATE_022) with non-zero RLE factors (1827 human and 1036 mouse libraries)

Enhancers#Data

Links to gene tables

List of key marker genes for each of the time-courses

  • extract from individual time-course pages
  • will be used to check each of the time-courses

List of early response marker genes

List of transcription factors

  • link to existing list

List of genes involved in epigenetics

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