Publications - Supplemental material
Please find below supplemental material corresponding to publications of our group. Currently, we list 133 supplements.
If you have problems accessing electronic information, please let us know:
You may use this URL to cite or link to us.
©NOTICE: All documents are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.
This supplement is also available at http://www.bioinf.uni-leipzig.de/publications/supplements/13-001You may use this URL to cite or link to us.
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
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.
Supplementary methods, figures, and tables [PDF]
Differentially expressed TARs in hg19 (DE-TARs)- Cell cycle regulated
- G0 versus G1 [BED:all] [BED:bona fide non-coding DE-TARs]
- G1 versus S [BED:all] [BED:bona fide non-coding DE-TARs]
- S versus G2 [BED:all] [BED:bona fide non-coding DE-TARs]
- G0 versus G2 [BED:all] [BED:bona fide non-coding DE-TARs]
- P53 regulated
- D53wt cells with defunct endogenous P53 versus 53wt cells stably transfected with P53 wild type [BED:all] [BED:bona fide non-coding DE-TARs]
- Stat-3 regulated
- INA-6 cells deprived from IL-6 for 13h versus INA-6 cells after one hour of restimulation [BED:all] [BED:bona fide non-coding DE-TARs]
- INA-6 cells deprived from IL-6 for 13h versus INA-6 cells permanently cultured in presence of IL-6 [BED:all] [BED:bona fide non-coding DE-TARs]
- INA-6 cells restimulated for one hour versus INA-6 cells permanently cultured in presence of IL-6 [BED:all] [BED:bona fide non-coding DE-TARs]
- Expressed within cell cycle (HFF cells):
- Expressed in D53wt cells:
- Expressed in INA-6 cells:
- Cell cycle regulated
- G0 versus G1 [BED:up-regulated] [BED:down-regulated]
- G1 versus S [BED:up-regulated] [BED:down-regulated]
- S versus G2 [BED:up-regulated] [BED:down-regulated]
- G0 versus G2 [BED:up-regulated] [BED:down-regulated]
- P53 regulated
- D53wt cells with defunct endogenous P53 versus 53wt cells stably transfected with P53 wild type [BED:up-regulated] [BED:down-regulated]
- Stat-3 regulated
- INA-6 cells deprived from IL-6 for 13h versus INA-6 cells after one hour of restimulation [BED:up-regulated] [BED:down-regulated]
- INA-6 cells deprived from IL-6 for 13h versus INA-6 cells permanently cultured in presence of IL-6 [BED:up-regulated] [BED:down-regulated]
- INA-6 cells restimulated for one hour versus INA-6 cells permanently cultured in presence of IL-6 [BED:up-regulated] [BED:down-regulated]
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.
- Bona fide non-coding probe in intergenic space [CSV]
- Bona fide non-coding probe in intronic space [CSV]
- Bona fide non-coding probe antisense to protein-coding gene [CSV]