Time-courses resources

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)

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

• 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