Evaluation of the RNA-dependence of PRC2 binding to chromatin in human pluripotent stem cells

Polycomb Repressive Complex 2 (PRC2), an important histone modifier and epigenetic repressor, has been known to interact with RNA for almost two decades. In our previous publication (Long, Hwang et al. 2020), we presented data supporting the functional importance of RNA interaction in maintaining PRC2 occupancy on chromatin, using comprehensive approaches including an RNA-binding mutant of PRC2 and an rChIP-seq assay. Recently, concerns have been expressed regarding whether the RNA-binding mutant has impaired histone methyltransferase activity and whether the rChIP-seq assay can potentially generate artifacts. Here we provide new data that support a number of our original findings. First, we found the RNA-binding mutant to be fully capable of maintaining H3K27me3 levels in human induced pluripotent stem cells. The mutant had reduced methyltransferase activity in vitro, but only on some substrates at early time points. Second, we found that our rChIP-seq method gave consistent data across antibodies and cell lines. Third, we further optimized rChIP-seq by using lower concentrations of RNase A and incorporating a catalytically inactive mutant RNase A as a control, as well as using an alternative RNase (RNase T1). The EZH2 rChIP-seq results using the optimized protocols supported our original finding that RNA interaction contributes to the chromatin occupancy of PRC2.

Evolutionary divergence of Firre localization and expression

Long noncoding RNAs (lncRNAs) are rapidly evolving and thus typically poorly conserved in their sequences. How these sequence differences affect the characteristics and potential functions of lncRNAs with shared synteny remains unclear. Here we show that the syntenically conserved lncRNA Firre displays distinct expression and localization patterns in human and mouse. Single molecule RNA FISH reveals that in a range of cell lines, mouse Firre (mFirre) is predominantly nuclear, while human FIRRE (hFIRRE) is distributed between the cytoplasm and nucleus. This localization pattern is maintained in human/mouse hybrid cells expressing both human and mouse Firre, implying that the localization of the lncRNA is species autonomous. We find that the majority of hFIRRE transcripts in the cytoplasm are comprised of isoforms that are enriched in RRD repeats. We furthermore determine that in various tissues, mFirre is more highly expressed than its human counterpart. Our data illustrate that the rapid evolution of syntenic lncRNAs can lead to variations in lncRNA localization and abundance, which in turn may result in disparate lncRNA functions even in closely related species.

Genome-wide perturbations of Alu expression and Alu-associated post-transcriptional regulations distinguish oligodendroglioma from other gliomas

Alu is a primate-specific repeat element in the human genome and has been increasingly appreciated as a regulatory element in many biological processes. But the appreciation of Alu has been limited in tumorigenesis, especially for brain tumor. To investigate the relevance of Alu to the gliomagenesis, we studied Alu element-associated post-transcriptional processes and the RNA expression of the element by performing RNA-seq for a total of 41 pairs of neurotypical and diverse glioma brain tissues. We find that A-to-I editing and circular RNA levels, as well as Alu RNA expression, are decreased overall in gliomas, compared to normal tissue. Interestingly, grade 2 oligodendrogliomas are least affected in A-to-I editing and circular RNA levels among gliomas, whereas they have a higher proportion of down-regulated Alu subfamilies, compared to the other gliomas. These findings collectively imply a unique pattern of Alu-associated transcriptomes in grade 2 oligodendroglioma, providing an insight to gliomagenesis from the perspective of an evolutionary genetic element.

Clinical and electrophysiological characteristics of extra-pulmonary vein triggers in patients who underwent catheter ablation for atrial fibrillation

Funding Acknowledgements

Type of funding sources: None.

Background

Extra-pulmonary vein (PV) triggers play significant roles in atrial fibrillation (AF) recurrence after AF catheter ablation (AFCA).

Purpose

We explore the clinical and electrophysiological characteristics of extra-PV triggers in de novo and repeat-AFCA procedure.

Methods

We included 2,151 patients who had de novo AFCA and 319 repeat AFCA (female 28.0%, 59.1 ± 10.8 years old, paroxysmal AF 65.1%) those underwent post-procedural isoproterenol (ISO) provocation tests. We analysed the clinical, electrophysiological, and procedure-related factors associated with extra-PV triggers.

Results

Extra-PV triggers were documented in 11.9% (1.19 ± 0.42 foci) after de novo-AFCA and 27.0% (1.37 ± 0.65 foci) after repeat-AFCA (p = 0.004). LA volume index (OR 1.02 [1.01-1.03], p = 0.004), history of vascular disease (OR 0.55[0.31-0.91], p = 0.028) and Lead I amplitude of electrocardiogram (OR <0.01 [<0.01-0.62], p = 0.032) were independently associated with the existence of extra-PV triggers in de-novo procedure. Women (OR 1.84 [1.03-3.25], p = 0.037) and LA appendage volume (OR 1.04 [1.01-1.07] p = 0.027) were independently associated with extra-PV triggers during the redo-mapping procedure. Septum (28.4%), coronary sinus (24.0%), and superior vena cava (19.6%) were common extra-PV foci, and septal foci were more commonly found in repeat mapping (38.4% vs. 25.0%, p = 0.025). Among 65 patients who showed extra-PV at the repeat procedures, 19 (29.2%) matched with previous focal or empirical extra-PV ablation sites and 9 (13.8%) were multiple or unmappable sites. AF recurrence rates were significantly higher in both patients with extra-PV triggers after de novo procedures (Log-rank P <0.001; HR 1.93 [1.58-2.36], p= <0.001) and repeat procedures (Log-rank P <0.001, HR 1.87 [1.29-2.70], p= <0.001).

Conclusion

ISO provoked extra-PV triggers commonly found in AF patients with significant remodelling and previous empirical or focal extra-PV ablations. Existence of extra-PV triggers were independently associated with poorer rhythm outcome after both de novo and repeat AFCA. Denovo AF ablation outcome OverallExtra-PV triggers (-)Extra-PV triggers (+)p-value(n = 2151)(n = 1895)(n = 256)Age, yrs58.98 ± 10.9558.73 ± 11.0360.76 ± 10.200.006Male, (%)1550 ( 72.1)1389 ( 73.3)161 ( 62.9)0.001Follow up duration, month50.30 (37.71)51.65 (37.95)40.71 (34.58)<0.001Early recurrence (%)579 ( 27.8)455 ( 24.9)124 ( 48.4)<0.001Clinical recurrence (%)699 ( 33.6)584 ( 32.0)115 ( 44.9)<0.001Abstract Figure. AF free survival according to Extra PVT

Long-term outcomes of empirical extra-pulmonary vein linear ablation in patients with persistent atrial fibrillation

Funding Acknowledgements

Type of funding sources: Public grant(s) – National budget only. Main funding source(s): This work was supported by grants [HI18C0070] and [HI19C0114] from the Korea Health 21 R&D Project, Ministry of Health and Welfare, and a grant [NRF-2020R1A2B01001695] from the Basic Science Research Program run by the National Research Foundation of Korea (NRF).

Background

Although extra-pulmonary vein (PV) left atrial (LA) linear ablation has been performed during catheter ablation (CA) of persistent atrial fibrillation (PeAF), the long-term efficacy and safety of this procedure have not yet been verified.

Purpose

We investigated whether an anterior line (AL) and posterior box ablation (POBA) in addition to circumferential PV isolation (CPVI) improves the rhythm without worsening the LA function in PeAF patients.

Methods

We retrospectively compared the additional AL + POBA and CPVI alone groups in 604 patients with PeAF who underwent regular rhythm follow-ups (16.9%; males 79.3%, 58.5 ± 10.7 years of age) after propensity score matching. The primary endpoint was AF recurrence after single procedures and secondary endpoints were the cardioversion rate, response to anti arrhythmic drugs, LA changes, and re-conduction rates of the de-novo ablation lesion set.

Results

After a mean follow-up of 45.2 ± 33.6 months, the clinical recurrence rate did not significantly differ between the two groups (log-rank p = 0.554) despite longer procedure times in the AL + POBA group (p < 0.001). Atrial tachycardia recurrences (p = 0.001) and the cardioversion rates after ablation (p < 0.001) were higher in the AL + POBA group than CPVI group. AL + POBA was associated with better rhythm outcomes in patients with large anterior LA volume indices (p for interaction 0.037) and low mean LAA(left atrial appendage) voltages (p for interaction 0.019). In repeat procedures, the LA pulse pressure elevation was significant after the AL + POBA.

Conclusion

In patients with PeAF, an AL + POBA in addition to the CPVI did not improve the rhythm outcomes nor influence the long-term safety, and lead to more extended procedures. Procedure outcomes OverallAL + POBACPVIp-value(n = 604)(n = 302)(n = 302)Procedure time, min190.8 ± 62.6226.9 ± 49.4154.6 ± 52.8<0.001Ablation time, sec5079 ± 19566420 ± 13723738± 1475<0.001Overall complications24 (4.0)13 (4.3)11 (3.6)0.835Early recurrence, n (%)277 (45.9)129 (42.7)148 (49.0)0.142Recurrence type AT, n (% in early recur)77 (27.8)51 (39.5)26 (17.6)<0.001Clinical recurrence within 1-year, n(%)116 (19.2)52 (17.2)65 (21.5)0.256Recurrence type AT, n (% in clinical recur)60 (23.1)46 (30.7)14 (12.7)0.001Cardioversion, n (% in total recur/ % overall)105 (40.4/17.4)74 (49.3/24.5)31 (28.1/10.3)<0.001POBA, posterior box ablation; AL, anterior line; CPVI, circumferential pulmonary vein isolation; AT, atrial tachycardia;Abstract Figure. Long term ablation outcome

Downstream changes in river avulsion style are related to channel morphology

One of the most dramatic events in river environments is the natural diversion, or avulsion, of a channel across its floodplain. Though rarely witnessed, avulsions can cause massive floods, and over geologic time they create most of the fluvial stratigraphic record. Avulsions exhibit behavior ranging from reoccupying abandoned channels to constructing new channels and splay complexes. To quantify avulsion behavior, or style, we measure avulsion-related floodplain disturbance in modern environments. We show that for 63 avulsions from Andean, Himalayan, and New Guinean basins, avulsion style correlates with channel morphology and changes systematically downstream. Avulsions in braided rivers reoccupy abandoned channels, whereas avulsions in meandering rivers often produce flooding and sediment deposition during channel construction. These downstream changes in avulsion style can explain the abrupt transition from channel-dominated to floodplain-dominated facies commonly observed in foreland basin stratigraphy. These dynamics also explain why some avulsions are more hazardous than others.

River avulsions are dramatic events that can cause the loss of many human lives. The authors here investigate how river avulsion style changes with river morphology, and how these changes impact flooding and stratigraphy.

The Sox2 transcription factor binds RNA

Certain transcription factors are proposed to form functional interactions with RNA to facilitate proper regulation of gene expression. Sox2, a transcription factor critical for maintenance of pluripotency and neurogenesis, has been found associated with several lncRNAs, although it is unknown whether these interactions are direct or via other proteins. Here we demonstrate that human Sox2 interacts directly with one of these lncRNAs with high affinity through its HMG DNA-binding domain in vitro. These interactions are primarily with double-stranded RNA in a non-sequence specific fashion, mediated by a similar but not identical interaction surface. We further determined that Sox2 directly binds RNA in mouse embryonic stem cells by UV-cross-linked immunoprecipitation of Sox2 and more than a thousand Sox2-RNA interactions in vivo were identified using fRIP-seq. Together, these data reveal that Sox2 employs a high-affinity/low-specificity paradigm for RNA binding in vitro and in vivo.

Some transcription factors have been proposed to functionally interact with RNA to facilitate proper regulation of gene expression. Here the authors demonstrate that human Sox2 interact directly and with high affinity to RNAs through its HMG DNA-binding domain.

Characterizing the nuclear and cytoplasmic transcriptomes in developing and mature human cortex uncovers new insight into psychiatric disease gene regulation

Transcriptome compartmentalization by the nuclear membrane provides both stochastic and functional buffering of transcript activity in the cytoplasm, and has recently been implicated in neurodegenerative disease processes. Although many mechanisms regulating transcript compartmentalization are also prevalent in brain development, the extent to which subcellular localization differs as the brain matures has yet to be addressed. To characterize the nuclear and cytoplasmic transcriptomes during brain development, we sequenced both RNA fractions from homogenate prenatal and adult human postmortem cortex using poly(A)+ and Ribo-Zero library preparation methods. We find that while many genes are differentially expressed by fraction and developmental expression changes are similarly detectable in nuclear and cytoplasmic RNA, the compartmented transcriptomes become more distinct as the brain matures, perhaps reflecting increased utilization of nuclear retention as a regulatory strategy in adult brain. We examined potential mechanisms of this developmental divergence including alternative splicing, RNA editing, nuclear pore composition, RNA-binding protein motif enrichment, and RNA secondary structure. Intron retention is associated with greater nuclear abundance in a subset of transcripts, as is enrichment for several splicing factor binding motifs. Finally, we examined disease association with fraction-regulated gene sets and found nuclear-enriched genes were also preferentially enriched in gene sets associated with neurodevelopmental psychiatric disorders. These results suggest that although gene-level expression is globally comparable between fractions, nuclear retention of transcripts may play an underappreciated role in developmental regulation of gene expression in brain, particularly in genes whose dysregulation is related to neuropsychiatric disorders.

The Firre locus produces a trans-acting RNA molecule that functions in hematopoiesis

RNA has been classically known to play central roles in biology, including maintaining telomeres, protein synthesis, and in sex chromosome compensation. While thousands of long noncoding RNAs (lncRNAs) have been identified, attributing RNA-based roles to lncRNA loci requires assessing whether phenotype(s) could be due to DNA regulatory elements, transcription, or the lncRNA. Here, we use the conserved X chromosome lncRNA locus Firre, as a model to discriminate between DNA- and RNA-mediated effects in vivo. We demonstrate that (i) Firre mutant mice have cell-specific hematopoietic phenotypes, and (ii) upon exposure to lipopolysaccharide, mice overexpressing Firre exhibit increased levels of pro-inflammatory cytokines and impaired survival. (iii) Deletion of Firre does not result in changes in local gene expression, but rather in changes on autosomes that can be rescued by expression of transgenic Firre RNA. Together, our results provide genetic evidence that the Firre locus produces a trans-acting lncRNA that has physiological roles in hematopoiesis.

Integrative analysis of DNA methylation suggests down-regulation of oncogenic pathways and reduced somatic mutation rates in survival outliers of glioblastoma

The study of survival outliers of glioblastoma can provide important clues on gliomagenesis as well as on the ways to alter clinical course of this almost uniformly lethal cancer type. However, there has been little consensus on genetic and epigenetic signatures of the long-term survival outliers of glioblastoma. Although the two classical molecular markers of glioblastoma including isocitrate dehydrogenase 1 or 2 (IDH1/2) mutation and O6-methylguanine DNA methyltransferase (MGMT) promoter methylation are associated with overall survival rate of glioblastoma patients, they are not specific to the survival outliers. In this study, we compared the two groups of survival outliers of glioblastoma with IDH wild-type, consisting of the glioblastoma patients who lived longer than 3 years (n = 17) and the patients who lived less than 1 year (n = 12) in terms of genome-wide DNA methylation profile. Statistical analyses were performed to identify differentially methylated sites between the two groups. Functional implication of DNA methylation patterns specific to long-term survivors of glioblastoma were investigated by comprehensive enrichment analyses with genomic and epigenomic features. We found that the genome of long-term survivors of glioblastoma is differentially methylated relative to short-term survivor patients depending on CpG density: hypermethylation near CpG islands (CGIs) and hypomethylation far from CGIs. Interestingly, these two patterns are associated with distinct oncogenic aspects in gliomagenesis. In the long-term survival glioblastoma-specific sites distant from CGI, somatic mutations of glioblastoma are enriched with higher DNA methylation, suggesting that the hypomethylation in long-term survival glioblastoma can contribute to reduce the rate of somatic mutation. On the other hand, the hypermethylation near CGIs associates with transcriptional downregulation of genes involved in cancer progression pathways. Using independent cohorts of IDH1/2- wild type glioblastoma, we also showed that these two patterns of DNA methylation can be used as molecular markers of long-term survival glioblastoma. Our results provide extended understanding of DNA methylation, especially of DNA hypomethylation, in cancer genome and reveal clinical importance of DNA methylation pattern as prognostic markers of glioblastoma.

Prediction of radiographic abnormalities by the use of bag-of-features and convolutional neural networks

This study evaluated the feasibility of bag-of-features (BOF) and convolutional neural networks (CNN) for computer-aided detection in distinguishing normal from abnormal radiographic findings. Computed thoracic radiographs of dogs were collected. For the purposes of this study, radiographic findings were used to distinguish between normal and abnormal in the following areas: (1) normal cardiac silhouette vs. cardiomegaly, (2) normal lung vs. abnormal lung patterns, (3) normal mediastinal position vs. mediastinal shift, (4) normal pleural space vs. pleural effusion, and (5) normal pleural space vs. pneumothorax. Images for training and testing the models consisted of ventrodorsal and lateral projection images of the same scale. The number of images used for each finding are as follow: 3142 for cardiomegaly (1571 normal and 1571 abnormal from 1143 dogs), 2086 for lung pattern (1043 normal and 1043 abnormal from 1247 dogs), 892 for mediastinal shift (446 normal and 446 abnormal from 387 dogs), 940 for pleural effusion (470 normal and 470 abnormal from 284 dogs), and 78 for pneumothorax (39 normal and 39 abnormal from 61 dogs). All data samples were divided so that 60% would be used for training the algorithms and 40% for testing the two models. The performance of the classifiers was evaluated by calculating the accuracy, sensitivity and specificity. The accuracy of both models ranged from 79.6% to 96.9% in the testing set. CNN showed higher accuracy (CNN; 92.9-96.9% and BOF; 79.6-96.9%) and sensitivity (CNN; 92.1-100% and BOF; 74.1-94.8%) than BOF. In conclusion, both BOF and CNN have potential to be useful for improving work efficiency by double reading.

Restoration of miR-29b exerts anti-cancer effects on glioblastoma

Background

Glioblastoma multiforme (GBM) is known as one of the most fatal forms of cancer. MicroRNAs have been widely implicated in the regulation of mammalian development and pathogenesis. The brain-enriched miR-29 subfamilies are known to be exclusively expressed in the developing brain, and they are aberrantly down-regulated in GBM. This study aims to elucidate the role of miR-29b in GBM development and the feasibility of therapeutic targeting using conjugated nanoparticles.

Methods

After confirmation of miR-29b expression levels in GBM tissues by analysis of open source data, the anticancer effect of miR-29b was tested by the introduction of syn-hsa-miR-29b-3p in the A172 GBM cell line. In vitro studies of cell viability and apoptosis and ex vivo study using GBM tissue slice cultures from 3 patients and nanoparticle delivery of miR-29b were performed.

Results

We discovered an increase in apoptotic cell populations with the introduction of miR-29b in the GBM cell line. An established human-derived GBM tissue slice culture system confirmed the anticancer effect of miR-29b-conjugated nanoparticles. Using PCR array, we found that exogenous miR-29b inhibits the expression of COL1A2, COL3A1, COL4A1, ELN, ITGA11, MMP24, and SPARC, which mediates an anticancer effect.

Conclusions

miR-29b may serve as a putative therapeutic molecule when its expression is restored using a nanoparticle delivery system in GBM.

Influence of heat and moisture treatment on carotenoids, phenolic content, and antioxidant capacity of orange maize flour

The aim of this work was to study the effect of heat and moisture treatment (HMT) on carotenoids, phenolic content and antioxidant capacity of ground, orange maize. Total carotenoid content (TCC) of untreated sample (53.39 mg/kg) was 2.2 times higher than measured in treated orange maize f (24.61 mg/kg). The rates of degradation with HMT were in the following order: β-carotene > β-cryptoxanthin > zeaxanthin > lutein. There was a significant interaction between longer heating time and higher moisture content on carotenoid degradation (p < .05). Total phenolic content (TPC) in raw sample (1664.74 mg/kg) was two-fold higher than in treated orange maize (827.89 mg/kg). Ferulic acid was the most abundant and stable phenolic acid in raw and treated orange maize. The antioxidant capacity of orange maize was higher in methanol than in butanol extracts. The highest correlation (0.924) was observed between TPC and ABTS+ scavenging capacity of methanol extracts.

Glutaminase 2 expression is associated with regional heterogeneity of 5-aminolevulinic acid fluorescence in glioblastoma

Fluorescence-guided surgery using 5-aminolevulinic acid (5-ALA) is now a widely-used modality for glioblastoma (GBM) treatment. However, intratumoral heterogeneity of fluorescence intensity may reflect different onco-metabolic programs. Here, we investigated the metabolic mechanism underlying the heterogeneity of 5-ALA fluorescence in GBM. Using an in-house developed fluorescence quantification system for tumor tissues, we collected 3 types of GBM tissues on the basis of their fluorescence intensity, which was characterized as strong, weak, and none. Expression profiling by RNA-sequencing revealed 77 genes with a proportional relationship and 509 genes with an inverse relationship between gene expression and fluorescence intensity. Functional analysis and in vitro experiments confirmed glutaminase 2 (GLS2) as a key gene associated with the fluorescence heterogeneity. Subsequent metabolite profiling discovered that insufficient NADPH due to GLS2 underexpression was responsible for the delayed metabolism of 5-ALA and accumulation of protoporphyrin IX (PpIX) in the high fluorescence area. The expression level of GLS2 and related NADPH production capacity is associated with the regional heterogeneity of 5-ALA fluorescence in GBM.

A phase II study of gemcitabine-based chemoradiotherapy (CCRT) after triplet induction chemotherapy (ICT) for locally advanced pancreatic cancer (LAPC): A Taiwan Cooperative Oncology Group (TCOG) study

e15562

The optimal management of LAPC remains controversial. The efficacy of CCRT is hampered by early systemic dissemination. To treat undetectable metastases and to select patients who are likely to benefit from CCRT, ICT followed by CCRT has recently been extensively evaluated in LAPC. Recently, we showed that triplet chemotherapy consisting of gemcitabine 800 mg/m2 (10 mg/m2/min) followed by oxaliplatin 85 mg/m2 and 48-hour infusion of 5-FU/LV 3,000 and 150 mg/m2 Q 2 weeks, the GOFL regimen, is feasible and active for pts with APC. Chemo-naïve pts with histo- /cytologically proven unresectable LAPC, and bi-dimensionally measurable diseases were eligible. Patients who did not experience disease progression (PD) after 6 cycles of GOFL would had CCRT consisting of weekly gemcitabine 400mg/m2 plus 50.4Gy/28 fractions of radiation 4–6 weeks later. After CCRT, pts were re-evaluated for surgical intervention and those with unresectable disease would continue GOFL until PD, unacceptable toxicity, patient's refusal or death. Among the 50 enrolled pts (24F/26M, median age 58.5 years), 48 had definitively unresectable diseases. After induction GOFL, 16 (32%) pts were off-studied because of PD in 12 (24%) and ICT-related toxicity in 4 (8%, PD/UE group). Among the 34 (68%) with objective response or stable disease after 6 cycles of ICT, 27 (54%) who completed the assigned multimodality treatment are categorized as CCRT group; whiles 7 (14%) who either declined CCRT (in 5) or still on ICT (in 2) are categorized as non-CCRT group. The median PFS and OS for the ITT population were 9.1 and 14.5 months, respectively. The median PFS for PD/UE, non-CCRT and CCRT groups were 2.1, 8.2 and 12.8 months, respectively; whiles the OS were 8.5, 15.0 and 18.3 months, respectively. The most common grade 3–4 toxicities were neutropenia (40%), anemia (14%), infection (16%), nausea (26%), vomiting (20%). Grade 2–3 peripheral neuropathy was observed in 7 of 29 who received post-CCRT GOFL. Conclusion: Three months of triplet ICT followed by gemcitabine-based CCRT is feasible and likely to prolong the survival of selected LAPC pts. Prospective, randomization study is warranted to validate the findings.

No significant financial relationships to disclose.

Identification of differentially expressed subnetworks based on multivariate ANOVA

Background

Since high-throughput protein-protein interaction (PPI) data has recently become available for humans, there has been a growing interest in combining PPI data with other genome-wide data. In particular, the identification of phenotype-related PPI subnetworks using gene expression data has been of great concern. Successful integration for the identification of significant subnetworks requires the use of a search algorithm with a proper scoring method. Here we propose a multivariate analysis of variance (MANOVA)-based scoring method with a greedy search for identifying differentially expressed PPI subnetworks.

Results

Given the MANOVA-based scoring method, we performed a greedy search to identify the subnetworks with the maximum scores in the PPI network. Our approach was successfully applied to human microarray datasets. Each identified subnetwork was annotated with the Gene Ontology (GO) term, resulting in the phenotype-related functional pathway or complex. We also compared these results with those of other scoring methods such as t statistic- and mutual information-based scoring methods. The MANOVA-based method produced subnetworks with a larger number of proteins than the other methods. Furthermore, the subnetworks identified by the MANOVA-based method tended to consist of highly correlated proteins.

Conclusion

This article proposes a MANOVA-based scoring method to combine PPI data with expression data using a greedy search. This method is recommended for the highly sensitive detection of large subnetworks.