Time-courses resources: Difference between revisions
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=== List of early response marker genes === |
=== List of early response marker genes === |
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*extracte from literature |
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*will be used to check each of the time-courses |
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*Version 1.0 - Please see the README file for details, and send any feedback to [mailto:finn.drablos@ntnu.no Finn Drablos]. |
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(put link here) |
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*''Potential'' immediate and early response (IER) genes extracted from literature. |
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**The README file - [[File:README_IER_genes_1.0.txt]] |
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**The list of potential IER genes - [[File:Potential_IER_genes_1.0.xls]] |
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**The source data (publications) - [[File:Source_data_IER_1.0.xls]] |
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**Visualization of overlap between list and F5 time course data (Erik Arner) [[File:Ier_updown.pdf]] |
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=== List of transcription factors === |
=== List of transcription factors === |
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**The histone genes - [[File:EpiGenes_histones_1.0.txt]] |
**The histone genes - [[File:EpiGenes_histones_1.0.txt]] |
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**Genes considered, but not included - [[File:EpiGenes_removed_1.0.txt]] |
**Genes considered, but not included - [[File:EpiGenes_removed_1.0.txt]] |
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*Version 1.1 - Added mouse orthologs to the lists of human genes. Now stored in Excel format. |
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**The README file - [[File:README_EpiGenesDB_1.1.txt]] |
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**The main gene list - [[File:EpiGenes_main_1.1.xls]] |
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**The histone genes - [[File:EpiGenes_histones_1.1.xls]] |
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**Genes considered, but not included - [[File:EpiGenes_removed_1.1.xls]] |
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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)
- 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
- Version 1.0 - Please see the README file for details, and send any feedback to 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
- 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
- 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
