Time-courses resources: Difference between revisions
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*for all time courses (phase 2) |
*for all time courses (phase 2) |
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*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 |
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(put link here) |
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*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 |
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=== Expression table 2 === |
=== Expression table 2 === |
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Revision as of 16:24, 27 February 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)
- 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
- 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
- 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)
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
- extracte from literature
- will be used to check each of the time-courses
(put link here)
List of transcription factors
- 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 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
