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BIOINF 13-001: Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro ncRNAs

Jörg Hackermüller, Kristin Reiche, Christian Otto, Nadine Hösler, Katja Brocke-Heidrich, Levin Böhlig, Katharina Kasack, Peter Ahnert, Wolfgang Krupp, Kurt Engeland, Peter F. Stadler, Friedemann Horn

Supplementary methods, figures, and tables [PDF]

Differentially expressed TARs in hg19 (DE-TARs)
  1. Cell cycle regulated
  2. P53 regulated
  3. Stat-3 regulated
Transcriptionally active macroRNAs in hg19
  1. Expressed within cell cycle (HFF cells):
    • G0 (resting phase) [BED]
    • G1 phase [BED]
    • S phase [BED]
    • G2 phase [BED]
  2. Expressed in D53wt cells:
    • D53wt cells with defunct endogenous P53 [BED]
    • D53wt cells stably transfected with tetracycline responsive wild type P53 [BED]
  3. Expressed in INA-6 cells:
    • INA-6 cells deprived from IL-6 for 13h [BED]
    • INA-6 cells after one hour of restimulation [BED]
    • INA-6 cells permanently cultured in presence of IL-6 [BED]
Differentially expressed macro RNAs in hg19
  1. Cell cycle regulated
  2. P53 regulated
  3. Stat-3 regulated
Pairs of ncRNAs and closest mRNA

Pairs of bona fide non-coding probes and protein-coding genes (Gencode v12) with closest genome coordinates and both significantly differentially expressed between clinical samples of astrocytoma of grade I versus samples of astrocytoma of aggressive grades (grades III or IV, FDR<0.05). A fold change larger than 0 denotes high expression in tissue samples of grade I and low expression in samples of aggressive grades, i.e. logFC < 0 ≡ Grade I < Aggressive. A fold change less than 0 denotes low expression in grade I and high expression in aggressive grades, i.e. logFC > 0 ≡ Grade I > Aggressive.
  1. Bona fide non-coding probe in intergenic space [CSV]
  2. Bona fide non-coding probe in intronic space [CSV]
  3. Bona fide non-coding probe antisense to protein-coding gene [CSV]
R tool stairFinder [R]