Alcohol consumption, variability in alcohol dehydrogenase genes and risk of renal cell carcinoma.

Alcohol consumption has been associated inversely with renal cell carcinoma (RCC) risk; however, no study has examined effect modification by germline variation in alcohol-metabolizing genes. We investigated whether the association between alcohol intake and RCC risk is modulated by germline variants in alcohol dehydrogenase genes in a large case-control study. Data from 652 RCC cases and 1,366 non-cancer controls were analyzed. Alcohol intake was assessed using a standardized risk factor questionnaire. Three previously genotyped polymorphisms in ADH6 and ADH7 with the TaqMan assay were examined. Odds ratios (ORs) and 95% confidence interval (CI) were calculated using logistic regression, adjusting for covariates. Compared to non-drinkers, ever consumption of alcohol was associated with lower RCC risk (OR = 0.52, 95% CI = 0.42-0.65). Analysis with cubic spline regression curve showed a "J-shaped" relationship between alcohol drinks/day and RCC risk, such that there was no added benefit against RCC for consumption of more than two drinks/day. We observed effect modification by variation in rs1154454 (ADH7) (pinteraction = 0.007); a per unit increase in alcohol drink/day was associated with 35% lower RCC risk among non-minor allele carriers, a 27% lower risk among those who carry one copy of the minor allele, but no association was observed among those with two copies of the minor allele. These findings indicate that alcohol consumption is associated with lower RCC risk. Consuming more than two drinks a day does not confer additional protection against RCC. The association between alcohol intake and RCC risk appears to be modulated by inter-individual germline variation in alcohol-metabolizing genes.

Coffee consumption and risk of renal cell carcinoma.

BACKGROUND: Studies have suggested an inverse association between coffee consumption and risk of renal cell carcinoma (RCC); however, data regarding decaffeinated coffee are limited. METHODS: We conducted a case-control study of 669 incident RCC cases and 1,001 frequency-matched controls. Participants completed identical risk factor questionnaires that solicited information about usual coffee consumption habits. The study participants were categorized as non-coffee, caffeinated coffee, decaffeinated coffee, or both caffeinated and decaffeinated coffee drinkers. Odds ratios (ORs) and 95% confidence intervals (CIs) were calculated using logistic regression, adjusting for multiple risk factors for RCC. RESULTS: Compared with no coffee consumption, we found an inverse association between caffeinated coffee consumption and RCC risk (OR 0.74; 95% CI 0.57-0.99), whereas we observed a trend toward increased risk of RCC for consumption of decaffeinated coffee (OR 1.47; 95% CI 0.98-2.19). Decaffeinated coffee consumption was associated also with increased risk of the clear cell RCC (ccRCC) subtype, particularly the aggressive form of ccRCC (OR 1.80; 95% CI 1.01-3.22). CONCLUSIONS: Consumption of caffeinated coffee is associated with reduced risk of RCC, while decaffeinated coffee consumption is associated with an increase in risk of aggressive ccRCC. Further inquiry is warranted in large prospective studies and should include assessment of dose-response associations.

Reconstruction of protein networks from an atlas of maize seed proteotypes.

A comprehensive knowledge of proteomic states is essential for understanding biological systems. Using mass spectrometry, we mapped an atlas of developing maize seed proteotypes comprising 14,165 proteins and 18,405 phosphopeptides (from 4,511 proteins), quantified across eight tissues. We found that many of the most abundant proteins are not associated with detectable levels of their mRNAs, and we provide evidence for three potential explanations: transport of proteins between tissues; diurnal, out-of-phase accumulation of mRNAs and cognate proteins; and differential lifetimes of mRNAs compared with proteins. Likewise, many of the most abundant mRNAs were not associated with detectable levels of their proteins. Across the entire dataset, protein abundance was poorly correlated with mRNA levels and was largely independent of phosphorylation status. Comparisons between proteotypes revealed the quantitative contribution of specific proteins and phosphorylation events to the spatially and temporally regulated starch and oil biosynthetic pathways. Reconstruction of signaling networks established associations of proteins and phosphoproteins with distinct biological processes acting during seed development. Additionally, a protein kinase substrate network was reconstructed, enabling the identification of 762 potential substrates of specific protein kinases. Finally, examination of 694 transcription factors revealed remarkable constraints on patterns of expression and phosphorylation within transcription factor families. These results provide a resource for understanding seed development in a crop that is the foundation of modern agriculture.

Transforming primary care in the New Orleans safety-net: the patient experience.

BACKGROUND: The patient-centered medical home (PCMH) is a key service delivery innovation in health reform. However, there are growing questions about whether the changes in clinics promoted by the PCMH model lead to improvements in the patient experience. OBJECTIVE: To test the hypothesis that PCMH improvements in safety-net primary care clinics are associated with a more positive patient experience. RESEARCH DESIGN: Multilevel cross-sectional analysis of patients nested within the primary care clinics that serve them. SUBJECTS: Primary care clinic leaders and patients throughout the City of New Orleans health care safety-net. MEASURES: Dependent variables included patient ratings of accessibility, coordination, and confidence in the quality/safety of care. The key independent variable was a score measuring PCMH structural and process improvements at the clinic level. RESULTS: Approximately two thirds of patients in New Orleans gave positive ratings to their clinics on access and quality/safety, but only one third did for care coordination. In all but the largest clinics, patient experiences of care coordination were positively associated with the clinic's use of PCMH structural and process changes. Results for patient ratings of access and quality/safety were mixed. CONCLUSIONS: Among primary care clinics in the New Orleans safety-net, use of more PCMH improvements at the clinic level led to more positive patient rating of care coordination, but not of accessibility or confidence in quality/safety. Ongoing efforts to pilot, demonstrate, implement, and evaluate the PCMH should consider how the impact of medical practice transformation could vary across different aspects of the patient experience.

Comparison of baseline quality of life measures between renal cell carcinoma patients undergoing partial versus radical nephrectomy.

BACKGROUND: To compare demographics, pathologic features, performance scores, comorbidities, symptoms and responses to quality of life (QoL) surveys between nephron-sparing surgery (NSS) and radical nephrectomy (RN) patients prior to surgical intervention. Previous investigators have compared QoL outcomes for patients undergoing RN and NSS; however, there are limited data comparing QoL-related characteristics at baseline between these groups. METHODS: We identified 144 patients with localized RCC who underwent either NSS (n = 71) or RN (n = 73) between May '07-November '12. We abstracted baseline data on demographic and clinic-pathologic variables as well as responses to the SF-36 and FACT-G surveys from our prospective registry. We amended the FACT-G with 8 additional questions designed to address RCC-specific QoL. For comparisons between the two groups, we employed Wilcoxon rank-sum and Fisher's Exact tests where appropriate. RESULTS: We observed RN patients to have more aggressive pathology. We noted no difference in performance scores between the two groups; however, RN patients were more likely to have higher Charlson scores (p = 0.022) and various symptoms at presentation (all p <0.001). For the QoL surveys, we did not observe differences on the FACT-G; however, we noted evidence of differential scores between the two groups on specific domains of the SF-36 (e.g. Mental Health; p 0.022) and the RCC-specific QoL questions added to the FACT-G. CONCLUSIONS: We report baseline differences between RN and NSS patients on clinico-pathologic as well as QoL-related metrics. As issues of survivorship become increasingly important, our results underscore the need to consider baseline status in evaluations of QoL-related outcomes for patients undergoing surgery for RCC.

Evaluation of MDM2, p16, and p53 staining levels as biomarkers of biochemical recurrence following salvage radiation therapy for recurrent prostate cancer.

BACKGROUND AND PURPOSE: The selection of appropriate candidates for salvage radiation therapy (SRT) to address a rising PSA following radical prostatectomy remains challenging. Herein, we provide the first evaluation of the ability of staining levels of the tumor based biomarkers MDM2, p16, and p53 to aid in prediction of biochemical recurrence (BCR) among men undergoing SRT for recurrent prostate cancer. MATERIAL AND METHODS: We identified 152 patients who were treated with SRT between July 1987 and July 2003. Staining levels of MDM2, p16, and p53 in primary tumor samples removed during prostatectomy were detected using monoclonal antibodies and quantified by use of a computer-assisted method. Associations of staining levels with BCR were evaluated using Cox proportional hazards regression models; relative risks (RRs) and 95% confidence intervals (CIs) were estimated. RESULTS: Compared to patients with low staining (≤median) as measured by percentage of cells with nuclear staining, there was no significant difference in risk of BCR for patients with high MDM2 staining (RR: 0.90, 95% CI: 0.57-1.45, P = 0.67), high p16 staining (RR: 0.88, 95% CI: 0.54-1.44, P = 0.62), or high p53 staining (RR: 1.33, 95% CI: 0.84-2.11, P = 0.23) in multivariable analysis. These results were consistent when considering alternate percentile cutpoints and alternate quantifications of biomarker staining. CONCLUSIONS: Our results provide evidence that MDM2, p16, and p53 staining levels are not useful in the prediction of BCR after SRT. As such, these biomarkers are of little clinical use in the selection of appropriate candidates for SRT.

RhoB mediates antitumor synergy of combined ixabepilone and sunitinib in human ovarian serous cancer.

OBJECTIVE: The aim was to evaluate antitumor activity of the combination of ixabepilone and sunitinib in pre-clinical models of chemotherapy naïve and refractory epithelial ovarian tumors, and to investigate the mechanism of synergy of such drug combination. METHODS: HOVTAX2 cell line was derived from a metastatic serous papillary epithelial ovarian tumor (EOC) and a paclitaxel-resistant derivative was established. Dose response curves for ixabepilone and sunitinib were generated and synergy was determined using combination indexes. The molecular mechanism of antitumor synergy was examined using shRNA silencing. RESULTS: The combination of ixabepilone and sunitinib demonstrated robust antitumor synergy in naïve and paclitaxel-resistant HOVTAX2 cell lines due to increased apoptosis. The GTPase, RhoB, was synergistically upregulated in cells treated with ixabepilone and sunitinib. Using shRNA, RhoB was demonstrated to mediate antitumor synergy. These results were validated in two other EOC cell lines. CONCLUSIONS: Ixabepilone plus sunitinib demonstrated antitumor synergy via RhoB in naïve and paclitaxel-resistant cells resulting in apoptosis. This study demonstrates a novel mechanism of action leading to antitumor synergy and provides 'proof-of-principle' for combining molecular targeted agents with cytotoxic chemotherapy to improve antitumor efficacy. RhoB could be envisioned as an early biomarker of response to therapy in a planned Phase II clinical trial to assess the efficacy of ixabepilone combined with a receptor tyrosine kinase inhibitor such as sunitinib. To the best of our knowledge, this is the first demonstration of antitumor synergy between these two classes of drugs in EOC and the pivotal role of RhoB in this synergy.

Locally advanced invasive lobular carcinoma presenting as skin erythema, with multimodality imaging correlation.

Invasive lobular carcinoma comprises 10-15% of invasive carcinomas of the breast. Its inconspicuous pattern of proliferation may lead to tumor manifestations that can be challenging to detect on mammography and clinical exam, which can result in tumor detection at advanced size and stage. This case demonstrates a locally advanced invasive lobular carcinoma and its subtle growth pattern illustrated on several imaging modalities, as well as its unique initial clinical presentation of skin erythema mistaken for rash.

Cytoplasmic sequestration of p27 via AKT phosphorylation in renal cell carcinoma.

PURPOSE: p27 localization and expression has prognostic and predictive value in cancer. Little is known regarding expression patterns of p27 in renal cell carcinoma (RCC) or how p27 participates in disease progression or response to therapy. EXPERIMENTAL DESIGN: RCC-derived cell lines, primary tumors, and normal renal epithelial cells were analyzed for p27 expression, phosphorylation (T157 of the NLS), and subcellular localization. RCC-derived cell lines were treated with phosphatidylinositol 3-kinase (PI3K) and mammalian target of rapamycin (mTOR) inhibitors and effects on p27 localization were assessed. The potential contribution of cytoplasmic p27 to resistance to apoptosis was also evaluated. RESULTS: p27 was elevated in tumors compared with matched controls, and cytoplasmic mislocalization of p27 was associated with increasing tumor grade. Cytoplasmic localization of p27 correlated with phosphorylation at T157, an AKT phosphorylation site in the p27 NLS. In RCC cell lines, activated PI3K/AKT signaling was accompanied by mislocalization of p27. AKT activation and phosphorylation of p27 was associated with resistance to apoptosis, and small interfering RNA knockdown of p27 or relocalization to the nucleus increased apoptosis in RCC cells. Treatment with the PI3K inhibitors LY294002 or wortmannin resulted in nuclear relocalization of p27, whereas mTOR inhibition by rapamycin did not. CONCLUSIONS: In RCC, p27 is phosphorylated at T157 of the NLS, with increasing tumor grade associated with cytoplasmic p27. PI3K inhibition (which reduces AKT activity) reduces T157 phosphorylation and induces nuclear relocalization of p27, whereas mTOR inhibition does not. Clinical testing of these findings may provide a rational approach for use of mTOR and PI3K/AKT pathway inhibitors in patients with RCC.

Effect of Leg Length-Evening Device on Perceived Balance in Patients Wearing a Controlled Ankle Motion Boot.

BACKGROUND: Patients are often made weightbearing as tolerated (WBAT) in a controlled ankle motion (CAM) boot for the management of various foot and ankle conditions. The CAM boot causes a leg length discrepancy (LLD) between the booted (longer) and contralateral (shorter) lower extremities. This discrepancy can potentially cause balance problems, undue strain on joints, and discomfort in patients. We hypothesized that a leg length-evening orthotic placed on the plantar aspect of the contralateral shoe improves balance among patients who are WBAT in a CAM boot. METHODS: Patients made WBAT in a CAM boot were randomized to either the leg length-evening orthotic intervention group or to a control group in which patients wore a normal shoe of their choice. Patients were followed for 2 weeks and asked a series of questions pertaining to balance and pain experienced at their knees, hips, and back. Balance was the primary outcome and was scored from 0 (no difficulty with balance) to 10 (great difficulty with balance). Of 107 subjects enrolled and randomized, 95 (88.8%) completed the study, satisfying the a priori sample size requirement of 94 patients. There were no differences in baseline characteristics between groups (P > .05 for each). RESULTS: Intervention patients reported less difficulty with balance than control patients (intention-to-treat analysis: 2.0±1.5 vs 3.2±1.8, P = .001; as-treated analysis: 2.1±1.7 vs 3.0±1.7, P = .009). Intervention and control patients did not differ with respect to pain experienced at their knees, hips, or back, or in a composite total pain score (P > .05 for each). CONCLUSION: This multicenter randomized controlled trial found that adding a limb length-evening orthotic to the plantar aspect of the contralateral shoe in a patient that is WBAT in a CAM boot improved patient-reported self-assessment of balance. The trial was powered to identify a difference in the primary outcome measure of balance and may have been insufficiently powered to identify differences in knee, hip, back, or total pain. LEVEL OF EVIDENCE: Level II, prospective comparative study.

Mechanism of glycan receptor recognition and specificity switch for avian, swine, and human adapted influenza virus hemagglutinins: a molecular dynamics perspective.

Hemagglutinins (HA's) from duck, swine, and human influenza viruses have previously been shown to prefer avian and human glycan receptor analogues with distinct topological profiles, pentasaccharides LSTa (alpha-2,3 linkage) and LSTc (alpha-2,6 linkage), in comparative molecular dynamics studies. On the basis of detailed analyses of the dynamic motions of the receptor binding domains (RBDs) and interaction energy profiles with individual glycan residues, we have identified approximately 30 residue positions in the RBD that present distinct profiles with the receptor analogues. Glycan binding constrained the conformational space sampling by the HA. Electrostatic steering appeared to play a key role in glycan binding specificity. The complex dynamic behaviors of the major SSE and trimeric interfaces with or without bound glycans suggested that networks of interactions might account for species specificity in these low affinity and high avidity (multivalent) interactions between different HA and glycans. Contact frequency, energetic decomposition, and H-bond analyses revealed species-specific differences in HA-glycan interaction profiles, not readily discernible from crystal structures alone. Interaction energy profiles indicated that mutation events at the set of residues such as 145, 156, 158, and 222 would favor human or avian receptor analogues, often through interactions with distal asialo-residues. These results correlate well with existing experimental evidence, and suggest new opportunities for simulation-based vaccine and drug development.

Tumefactive Fat Necrosis with Multinucleate Giant Cell Reaction Mimicking Recurrent Renal Cell Carcinoma following Percutaneous Renal Cryoablation.

Multinucleate Giant Cell (GC) reaction is a biological response that occurs secondary to infection, an implanted foreign body, tissue injury, or inflammation. In rare instances GC reactions have been reported following tissue ablation. Multinucleate GC reactions and tumefactive fat necrosis both have the ability to mimic cancer recurrence or metastasis and can appear as enhancing masses. We discuss a case of a surgically resected retroperitoneal perinephric mass thought to be recurrent renal cell carcinoma (RCC) that was pathologically confirmed as tumefactive fat necrosis with multinucleate GC reaction 2 years following percutaneous cryoablation of a small renal mass.

Replication-independent histone deposition by the HIR complex and Asf1.

The orderly deposition of histones onto DNA is mediated by conserved assembly complexes, including chromatin assembly factor-1 (CAF-1) and the Hir proteins . CAF-1 and the Hir proteins operate in distinct but functionally overlapping histone deposition pathways in vivo . The Hir proteins and CAF-1 share a common partner, the highly conserved histone H3/H4 binding protein Asf1, which binds the middle subunit of CAF-1 as well as to Hir proteins . Asf1 binds to newly synthesized histones H3/H4 , and this complex stimulates histone deposition by CAF-1 . In yeast, Asf1 is required for the contribution of the Hir proteins to gene silencing . Here, we demonstrate that Hir1, Hir2, Hir3, and Hpc2 comprise the HIR complex, which copurifies with the histone deposition protein Asf1. Together, the HIR complex and Asf1 deposit histones onto DNA in a replication-independent manner. Histone deposition by the HIR complex and Asf1 is impaired by a mutation in Asf1 that inhibits HIR binding. These data indicate that the HIR complex and Asf1 proteins function together as a conserved eukaryotic pathway for histone replacement throughout the cell cycle.

Secreted frizzled-related protein 1 loss contributes to tumor phenotype of clear cell renal cell carcinoma.

PURPOSE: Incidence and mortality rates for renal cell carcinoma (RCC) have been rising for decades. Unfortunately, the molecular events that support RCC carcinogenesis remain poorly understood. In an effort to gain a better understanding of signaling events in clear cell RCC (cRCC), we investigated the antitumor activity of secreted frizzled-related protein 1 (sFRP1), a negative regulator of Wnt signaling. EXPERIMENTAL DESIGN: Genomic profiling of cRCC tumors and patient-matched normal tissues was done and confirmed using quantitative PCR and immunohistochemistry. Methylation-specific PCR was done on patient samples to evaluate the mechanism responsible for sFRP1 loss. sFRP1 expression was restored in cRCC cells and the effects on tumor phenotype were characterized. RESULTS: Genomic profiling, quantitative PCR, and immunohistochemistry indicated that loss of sFRP1 occurred in cRCC and papillary RCC patient tissues. Twelve Wnt-regulated genes were up-regulated in cRCC tissues, including c-myc and cyclin D1, potentiators of cell proliferation and survival. Methylation of the sFRP1 gene was one mechanism identified for attenuation of sFRP1 mRNA. Stable reexpression of sFRP1 in cRCC cells resulted in decreased expression of Wnt target genes, decreased growth in cell culture, inhibition of anchorage-independent growth, and decreased tumor growth in athymic nude mice. CONCLUSIONS: To our knowledge, this is the first report to show that stable restoration of sFRP1 expression in cRCC cells attenuates the cRCC tumor phenotype. Our data support a role for sFRP1 as a tumor suppressor in cRCC and that perhaps loss of sFRP1 is an early, aberrant molecular event in renal cell carcinogenesis.

Magnetic resonance conditional paramagnetic choke for suppression of imaging artifacts during magnetic resonance imaging.

Higher risk patient populations require continuous physiological monitoring and, in some cases, connected life-support systems, during magnetic resonance imaging examinations. While recently there has been a shift toward wireless technology, some of the magnetic resonance imaging devices are still connected to the outside using cabling that could interfere with the magnetic resonance imaging's radio frequency during scanning, resulting in excessive heating. We developed a passive method for radio frequency suppression on cabling that may assist in making some of these devices magnetic resonance imaging compatible. A barrel-shaped strongly paramagnetic choke was developed to suppress induced radio frequency signals which are overlaid onto physiological monitoring leads during magnetic resonance imaging. It utilized a choke placed along the signal lines, with a gadolinium solution core. The choke's magnetic susceptibility was modeled, for a given geometric design, at increasing chelate concentration levels, and measured using a vibrating sample magnetometer. Radio frequency noise suppression versus frequency was quantified with network-analyzer measurements and tested using cabling placed in the magnetic resonance imaging scanner. Temperature-elevation and image-quality reduction due to the device were measured using American Society for Testing and Materials phantoms. Prototype chokes with gadolinium solution cores exhibited increasing magnetic susceptibility, and insertion loss (S21) also showed higher attenuation as gadolinium concentration increased. Image artifacts extending <4 mm from the choke were observed during magnetic resonance imaging, which agreed well with the predicted ∼3 mm artifact from the electrochemical machining simulation. An accompanying temperature increase of <1 °C was observed in the magnetic resonance imaging phantom trial. An effective paramagnetic choke for radio frequency suppression during magnetic resonance imaging was developed and its performance demonstrated.

Magnetohydrodynamic Voltage Recorder for Comparing Peripheral Blood Flow.

Blood flow is a clinical metric for monitoring of cardiovascular diseases but current measurements methods are costly or uncomfortable for patients. It was shown that the interaction of the magnetic field (B 0) during MRI and blood flow in the body, through the magnetohydrodynamic (MHD) effect, produce voltages (V MHD) observable through intra-MRI electrocardiography (ECG), which are correlated with regional blood flow. This study shows the reproducibility of V MHD outside the MRI and its application in a portable flow monitoring device. To recreate this interaction outside the MRI, a static neodymium magnet (0.4T) was placed in between two electrodes to induce the V MHD in a single lead ECG measurement. V MHD was extracted, and integrated over to obtain a stroke volume metric. A smartphone-enabled device utilizing this interaction was developed in order to create a more accessible method of obtaining blood flow measurements. The portable device displayed a <6% error compared to a commercial recorder, and was able to successfully record V MHD using the 0.4T magnet. Exercise stress testing showed a V MHD increase of 23% in healthy subjects, with an 81% increase in the athlete. The study demonstrates a new device utilizing MHD interactions with body circulation to obtain blood flow metrics.

GATA2 expression and biochemical recurrence following salvage radiation therapy for relapsing prostate cancer.

OBJECTIVE: High GATA2 expression has been associated with an increased risk of poor clinical outcomes after radical prostatectomy; however, this has not been studied in relation to risk of biochemical recurrence (BCR) after salvage radiation therapy (SRT) for recurrent prostate cancer after radical prostatectomy. Our aim was to evaluate the association between protein expression levels of GATA2 in primary prostate cancer tumour samples and the risk of BCR after SRT. METHODS: 109 males who were treated with SRT were included. The percentage of cells with nuclear staining and GATA2 staining intensity were both measured. These two measures were multiplied together to obtain a GATA2 H-score (range 0-12) which was our primary GATA2 staining measure. RESULTS: In unadjusted analysis, the risk of BCR was higher for patients with a GATA2 H-score >4 (hazard ratio = 2.04, p = 0.033). In multivariable analysis adjusting for SRT dose, pre-SRT PSA, pathological tumour stage and Gleason score, this association weakened substantially (hazard ratio = 1.45, p = 0.31). This lack of an independent association with BCR appears to be the result of correlations between GATA2 H-score >4 and higher pre-SRT PSA (p = 0.021), higher Gleason score (p = 0.044) and more severe pathological tumour stage (p = 0.068). CONCLUSION: Higher levels of GATA2 expression appear to be a marker of prostate cancer severity; however, these do not provide independent prognostic information regarding BCR beyond that of validated clinicopathological risk factors. Advances in knowledge: A higher GATA2 expression level appears to be correlated with known measures of prostate cancer severity and therefore is likely not an independent marker of outcome after SRT.

Integration of omic networks in a developmental atlas of maize.

Coexpression networks and gene regulatory networks (GRNs) are emerging as important tools for predicting functional roles of individual genes at a system-wide scale. To enable network reconstructions, we built a large-scale gene expression atlas composed of 62,547 messenger RNAs (mRNAs), 17,862 nonmodified proteins, and 6227 phosphoproteins harboring 31,595 phosphorylation sites quantified across maize development. Networks in which nodes are genes connected on the basis of highly correlated expression patterns of mRNAs were very different from networks that were based on coexpression of proteins. Roughly 85% of highly interconnected hubs were not conserved in expression between RNA and protein networks. However, networks from either data type were enriched in similar ontological categories and were effective in predicting known regulatory relationships. Integration of mRNA, protein, and phosphoprotein data sets greatly improved the predictive power of GRNs.