Coverage of HIPPIE by novel datasets.

<p>Coverage of HIPPIE by novel datasets.</p

Coverage of HIPPIE and overlap by three technique specific datasets.

<p>Left: proteins. Right: PPIs. Y2H is yeast-two-hybrid, Coprep is anti-bait coimmunoprecipitation and MS is affinity capture mass spectrometry. The protein numbers show that Y2H can focus on many proteins that have not been targeted by the other two techniques. Together the three techniques already cover 80% of all proteins currently considered in HIPPIE (i.e. 80% of all proteins in HIPPIE participate in at least one Y2H, Coprep or MS experiment). However, the overlap in PPIs between these datasets and to the remainder of HIPPIE is much smaller indicating that PPI detection is technique specific. Nevertheless, one can appreciate that similar techniques have a bias towards detecting similar PPIs, here illustrated by the significant overlap between Coprep and MS and by the little overlap of Y2H to the other two techniques.</p

Distribution of HIPPIE confidence scores.

<p>Interactions with scores above 0.73 (black bars) constitute only 25% of all and could be considered high-confidence interactions. According to the design of the scoring function, such score implies that the interaction is supported by multiple evidence.</p

Scores for experiment types.

<p>Scores for experiment types.</p

PPI data sources integrated in HIPPIE.

<p>PPI data sources integrated in HIPPIE.</p

ERRα modulates expression and activity of LDH. <i>LDHA</i> and <i>LDHB</i> expression levels were measured by quantitative real-time PCR.

<p>The ratio of LDH activity to CS activity was determined under various conditions. Measurements were made 48 h after transfection or 10 days of treatment with XCT790 and results are presented relative to the control which was assigned a unit value. <i>LDHA</i> and <i>LDHB</i> expression levels, the mean <i>LDHA/LDHB</i> ratio (A) and the relative LDH activity (B) for RO82W-1 cells transfected with 50 ng ERRα or 50 ng ERRα and 50 ng PRC or empty vectors (Control). <i>LDHA, LDHB</i> expression levels and mean of the <i>LDHA/LDHB</i> ratio (C) and relative LDH activity (D) for FTC-133 cells treated with XCT790 or vehicle (Control). <i>LDHA, LDHB</i> expression levels and mean of the <i>LDHA/LDHB</i> ratio (E) and relative LDH activity (F) for FTC-133 cells transfected with control or ERRα siRNA. The results are the mean values±SD of three experiments performed in duplicate relative to controls. *: p≤0.05.</p

Potential ERRα response elements in <i>LDHB</i> and <i>LDHA</i> promoters (A) Potential ERRα binding sites numbered relative to the transcription starting site (TSS) (B) Chromatin ImmunoPrecipitation (ChIP) assay for <i>LDH</i> promoters in XTC.UC1 cells using a polyclonal ERRα antibody.

<p>Chromatin was immunoprecipitated with the indicated antibody and submitted to quantitative PCR. Results are expressed as fold change of enrichment compared to control IgG immunoprecipitated material. ERRα-IP was realized in duplicate and each sample was tested in triplicate for quantitative PCR. TFBS: transcription factor binding site.</p

ERRα inhibits <i>LDHB</i> promoter activity.

<p>(A) Different construction of the human LDHB promoter reporter plasmid. (B) RO82W-1 cells were transfected with the indicated promoter constructs together with the expression plasmid of ERRα and/or PRC. Luciferase activity was determined 48 h after transfection and normalized against renilla luciferase activity. Results, presented in Relative Light Units (RLU), are the mean values±SD of three experiments performed in duplicate. <b>*</b>: p≤0.05 versus cells transfected with plasmids controls and no ERRα or PRC.</p

ERRα and PRC coregulate the cell cycle and metabolism in thyroid cells.

<p>RO82W-1 cells transfected with ERRα and PRC or empty vector (Control) and analysed 72 h after transfection. Pangenomic microarray results for metabolism genes. Gene-expression levels are grouped by class and ordered according to their mean log level of expression (A) or color-coded in the matrix from green (underexpression) to red (overexpression) (B). Ten main gene ontologies (C). Cell proliferation and lactate levels in media (D).</p

Additional file 6: Table S4 of A roadmap of constitutive NF-ÎşB activity in Hodgkin lymphoma: Dominant roles of p50 and p52 revealed by genome-wide analyses

shows the overlap of NF-ÎşB subunit binding and DNAse I hypersensitive sites (DHS) in L1236 and GM12878 cells. (DOCX 13 kb