Open Access Highly Accessed Methodology article

Assessment of network perturbation amplitudes by applying high-throughput data to causal biological networks

Florian Martin1, Ty M Thomson3, Alain Sewer1*, David A Drubin3, Carole Mathis1, Dirk Weisensee2, Dexter Pratt3, Julia Hoeng1 and Manuel C Peitsch1

Author Affiliations

1 Philip Morris International R&D, Philip Morris Products S.A., Quai Jeanrenaud 5, Neuchâtel, 2000, Switzerland

2 Philip Morris International R&D, Philip Morris Research Laboratories GmbH, Fuggerstr.3, Cologne, 51149, Germany

3 Selventa, One Alewife Center, Cambridge, MA, 02140, USA

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BMC Systems Biology 2012, 6:54  doi:10.1186/1752-0509-6-54

Published: 31 May 2012

Additional files

Additional file 1:

The NF-κB-direct HYP. Each row of the table contains a causal statement describing the connection between NF-κB and one of its direct target genes.

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Additional file 2:

TNFα dose-dependent induction of NF-κB nuclear translocation.(a) Non-treated NHBE cells show a diffuse cytoplasmic staining of NF-κB (left) while after adding TNFα to the culture medium (right), the nucleus of stimulated cells is strongly labeled (magnification 10X/0.3); (b) NF-κB nuclear fluorescence intensity (FI) per dose of TNFα. For each group, the nuclear fluorescence intensity was measured in 500 cells per well of three replicates. Across-group comparisons by one-way ANOVA test were all p < 0.001.

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Additional file 3:

HYP scores versus NF-κB nuclear translocation. The NF-κB-direct HYP scores for each amplitude scoring method (Strength, GPI, EPI and MASS) and each time point (30 minutes, 2 hours, 4 hours, 24 hours) plotted against NF-κB nuclear translocation at 30 minutes. Score error bars represent the 95 % confidence interval as determined by the Uncertainty statistic. Error bars in NF-κB nuclear translocation represent the standard deviation of the mean nuclear translocation for three different fields of view of the same population of cells.

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Additional file 4:

Comparison of NF-κB-direct HYP scores with 20-gene NF-κB HYP scores. Transcriptomic data from TNFα-treated NHBE cells was scored using each scoring method (Strength, GPI, EPI and MASS) for (a) the NF-κB-direct HYP, (b) a HYP composed of 20 NF-κB-regulated genes reported to be TNFα-responsive in mouse 3 T3 fibroblast cells (NFKBIA, CASP4, CCL5, TNFAIP3, CCL2, ZFP36, RIPK2, TNFSF10, NFKBIE, IL6, CCL20, ICAM1, TNFRSF1A, TNFRSF1B, SQSTM1, NRG1, SOD1, IL1RL1, HIF1A, ERBB2) [19]. Error bars represent the 95 % confidence interval as determined by the Uncertainty statistic. Scores that failed the Specificity criterion (Specificity p-value > 0.05; 1000 comparable HYPs) are shaded in gray.

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Additional file 5:

The aggregated IKK/NF-κB signaling HYP. Each row of the table contains a causal statement extracted from the Selventa Knowledgebase and obtained from the aggregation of the individual HYPs of the IKK/NF-κB signaling causal network model (Additional file 6).

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Additional file 6:

The IKK/NF-κB signaling causal network model. The full causal model is given (top), along with a schematic of the basic model architecture (middle). CHUK, IKBKB, and IKBKG act as inhibitors of NFKBIA, NFKBIB, and NFKBIE, which are in turn inhibitors of NFKB1, NFKB2, and RELA. The nodes used in the model are listed under each section. The nodes in bold represent nodes that have downstream gene expression measurables in the knowledgebase, and the number of measurables is given in the square brackets (because the same downstream may be found under multiple nodes, these 1227 downstream measurables correspond to 992 unique measurables). The notations used in the knowledgebase are as follows: “CHUK P@S” represents CHUK phosphorylated at serine (where the residue is given if known), “CHUK P@ST” represents CHUK phosphorylated at serine or threonine (the exact residue is unknown), “kaof(CHUK)” represents the kinase activity of CHUK, “CHUK:IKBKB” represents the complex of CHUK and IKBKB proteins, “IkappaB kinase complex Hs” represents an aggregate of the various IκB kinases (CHUK, IKBKB, and IKBKG) in Homo sapiens (Hs), “degradationof(NFKBIA)” represents the process of NFKBIA degradation, and “taof(NFKB1)” represents the transcriptional activity of NFKB1.

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Additional file 7:

The TNF HYP. Each row of the table contains a causal statement extracted from the Selventa Knowledgebase and describes a gene known to be modulated by the TNFα treatment of cells.

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Additional file 8:

The E2F1-direct HYP. Each row of the table contains a causal statement extracted from the Selventa Knowledgebase and describes the connection between E2F1 and one of its direct target genes.

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Additional file 9:

CellTiter-Glo® measurements of cell numbers. CellTiter-Glo® fluorescence measurements of cell number after 24 hours of NHBE cell treatment with various doses of TNFα. Fluorescence intensity is reported as a percentage of the mock-treated sample, and error bars represent the standard deviation of the fluorescence intensity for three different fields of view of the same population of cells.

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Additional file 10:

Computing Specificity statistics. The histogram of MASS scores for HYPs comparable to the NF-κB-direct HYP (1 ng/mL TNFα treatment of NHBE cells for 0.5 hour). The top histogram resulted from selecting measurables at random from all measurables (Specificity p-value of 0), and the bottom histogram resulted from selecting measurables with comparable likelihood of modulation (Specificity p-value of 0.072). The solid line indicates the NF-κB-direct HYP MASS score. The Specificity p-value was computed by doubling the total fraction of counts that were greater than this score (the fraction of counts in the red boxes).

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