Adipose tissue transcriptomic signature highlights the pathological relevance of extracellular matrix in human obesity

In the paper

“Adipose loss leads to the improvement of the inflammatory profile [11], with a concomitant reduction of infiltrating macrophages [13].”

What the sources say

• Not checked yetcites [11] Clement K, Viguerie N, Poitou C, Carette C, Pelloux V, Curat CA, Sicard A, Rome S, Benis A, Zucker JD, Vidal H, Laville M, Barsh GS, Basdevant A, Štich V, Stich V, Cancello R, Langin D: Weight loss regulates inflammation-related genes in white adipose tissue of obese subjects. FASEB J. 2004, 18: 1657-1669. 10.1096/fj.04-2204com. source
• Supported

  The citation is attached to the reduction in infiltrating macrophages. The Results report a significant reduction three months after surgery-induced weight loss, and the Discussion describes it as accompanying an improved inflammatory profile in morbidly obese patients. The finding concerns subcutaneous white adipose tissue. (LLM, conf=0.93)

  cites [13] Cancello R, Henegar C, Viguerie N, Taleb S, Poitou C, Rouault C, Coupaye M, Pelloux V, Hugol D, Bouillot JL, Bouloumié A, Barbatelli G, Cinti S, Svensson PA, Barsh GS, Zucker JD, Basdevant A, Langin D, Clément K: Reduction of macrophage infiltration and chemoattractant gene expression changes in white adipose tissue of morbidly obese subjects after surgery-induced weight loss. Diabetes. 2005, 54: 2277-2286. 10.2337/diabetes.54.8.2277. source

In the paper

“Among various ECM components, several genes coding for members of the integrin family were found to be significantly induced and co-expressed in obese WAT, occupying central positions in the first co-expression module (Figure 4, module 1).”

In the paper

“While the genes up-regulated in the obese WAT were annotated mainly by structural and functional themes associated with the cellular membrane and the extracellular space, the down-regulated genes were annotated mostly by themes related to the intracellular domain.”

In the paper

“The functional analysis of these genes identified 704 genes (307 up- and 397 down-regulated) annotated with Gene Ontology (GO) categories [22], and 253 genes (101 up- and 152 down-regulated) annotated with categories of the Kyoto Encyclopedia of Genes and Genomes (KEGG) [23].”

What the sources say

• Not checked yetcites [22] Gene Ontology. [http://www.geneontology.org]
• Not checked yetcites [23] Kyoto Encyclopedia of Genes and Genomes. [http://www.genome.jp/kegg/]

In the paper

“The expression levels of two members of the carnitine/choline acetyltransferase family (CPT1A and CPT1B) involved in this rate limiting step across the mitochondrial inner membrane were decreased as well as that of the CRAT gene, which catalyzes the reversible transfer of acyl groups from an acyl-CoA thioester to carnitine and regulates the ratio of acylCoA/CoA in the mitochondrial compartments.”

In the paper

“Interestingly, module 2 also gathered several genes involved in the induction of apoptosis, such as the death-associated protein (DAP), the death-associated protein kinase 2 (DAPK2), and the serine/threonine kinase 17a (STK17A), a member of the DAP kinase-related apoptosis-inducing protein kinase family, as well as the apoptosis-inducing factor (SIVA1), TNFRSF1A-associated via death domain (TRADD)”

In the paper

“Our analysis revealed major and interrelated changes of WAT transcriptomic signature in obese human subjects, involving extracellular matrix (ECM), and inflammatory and adipose metabolic processes.”

In the paper

“A number of these genes showed significant co-expression with members of the integrin family and are known to be involved in the recruitment and activation of immune circulating cells, such as monocytes, lymphocytes or neutrophils.”

In the paper

“As shown in Figure 4, some ECM related genes were co-expressed with a set of inflammatory genes (module 1), while showing a significant inverse expression pattern to that of genes belonging to the metabolic module (module 2).”

In the paper

“This analysis showed that biological themes related to the extracellular space (module 1) were annotating genes predominantly expressed in the SVF of WAT, while the genes annotated with themes related to the intracellular domain (module 2) were expressed predominantly in mature adipocytes (Figures 1b, 2b and 3b).”

In the paper

“Among them, integrin alpha V (ITGAV), CD163 and CCL18, two markers of the alternative pathway of macrophage activation, heat shock protein 8 (HSPA8), and contactin associated protein 1 (CNTNAP1), involved in the activation of intracellular signaling pathways, were strongly related to several genes encoding enzymes of the lipolytic pathway”

• Also stated in: § The transcriptomic signature of the subcutaneous WAT in obese subjects · plain

  “and to genes related to apoptosis, such as death-associated protein kinase 2 (DAPK2) and non-metastatic cells 3 protein (NME3).”

In the paper

“Two distinct types of biological interaction modules (indicated hereafter as module 1 and module 2) have been identified, one associating structural components, processes and regulatory pathways related to cellular membranes and the extracellular space (module 1), while the other groups components, processes and pathways associated with the intracellular domain (module 2).”

In the paper

“Functional analysis of these genes identified 2,687 genes (1,390 up- and 1,297 down-regulated) annotated with GO categories, and 868 genes (450 up- and 418 down-regulated) annotated with KEGG categories.”

In the paper

“This analysis also highlighted a segregated transcriptomic interaction pattern in obese WAT, distinguishing two interaction modules: one (module 1) grouping inflammatory and ECM related processes and another (module 2) associating adipose metabolic functions and other themes related to apoptosis and protein synthesis processes.”

In the paper

“The examination of the genes grouped in these functions retrieved representatives from all classes of ECM components, such as structural proteins, including members of the collagen family and several precursors of collagen formation, adherent proteins, such as fibronectin 1 and its receptor, as well as laminin family members, glycosaminoglycans and proteoglycans (lumican (LUM)), and specialized”

What the sources say

• Not checked yetcites [20] Companion Website to this Study. [http://corneliu.henegar.info/projects/FunNet/genome_biol_2008/index.htm]

In the paper

“Sixty percent of these ECM-related genes demonstrated a similar variation of their expression patterns in both in vivo and in vitro conditions, a proportion significantly greater (p value < 0.05) than the overall percentage of genes sharing similar expression patterns among those demonstrating a significant differential expression in the human and cell studies.”

In the paper

“Associated with the down-regulation of genes coding for inflammation mediators, an important number of genes related to oxidative phosphorylation and various other mitochondrial enzymes, as well as genes coding for enzymes involved in the degradation of glycosaminoglycans and proteoglycans, registered a significantly increased expression after weight loss.”

In the paper

“Indeed, the majority of the genes up-regulated in WAT after gastric bypass were associated with structural themes (GO Cellular Component) related to the intracellular domain and organelles ('protein complex', 'cytoplasm', 'mitochondrion', 'endoplasmic reticulum', 'lysosome', 'actin cytoskeleton', 'cytosolic part'), while the down-regulated genes (Figure 8a) were mostly associated with cellular”

In the paper

“In addition, some metallopeptidases implicated in the degradation of other ECM components were equally induced, such as the matrix metallopeptidase 2 (MMP2), concomitantly with several metallopeptidase inhibitors from the tissue inhibitor of metalloproteinase family (TIMP1, TIMP2).”

In the paper

“A number of ECM components showed opposite expression patterns to those noted in the previous condition, some being induced by weight loss while others were down-regulated (online supplementary Table 2 [20]).”

What the sources say

• Not checked yetcites [20] Companion Website to this Study. [http://corneliu.henegar.info/projects/FunNet/genome_biol_2008/index.htm]

In the paper

“Ffibrosis quantification in the same subjects three months after bariatric surgery found no significant decrease of interstitial fibrosis, in spite of a significant down-regulation of the genes related to inflammatory and immune responses and extensive variations in the expression of genes involved in ECM remodeling.”

In the paper

“Interestingly, the surgery induced weight loss was associated with a major shift of the WAT regulatory and interaction patterns, which reversed the functional genomic profile of the obese WAT and dramatically increased the intensity of the interactions between up-regulated adipose metabolic processes and down-regulated inflammatory and immune responses.”

In the paper

“This segregated interaction pattern was also confirmed by the observation that a significant fraction of the genes composing module 1 were positively correlated with BMI, while most of the genes grouped in module 2 showed negative correlation with the degree of obesity.”

In the paper

“We observed the presence of NK and T lymphocytes in obese WAT, although they appeared to be less abundant than macrophage cells.”

In the paper

“Among them, we noted the induction of IL13RA1, a subunit of the IL13 receptor complex reported to play a role in the internalization of IL13, and a major profibrotic protein known to induce transforming growth factor beta, and also of the IL4 receptor, which binds IL13 and IL4 and represents another well recognized profibrotic cytokine.”

In the paper

“In agreement, human pre-adipocytes cultured in the presence of AcMCs increased their production of fibronectin and collagen type I, which formed a fibrous network around the pre-adipocytes.”

In the paper

“Collagen type I and fibronectin were over-expressed in AcMC-conditioned media and organized in a fiber network structure (Figure 14a-d).”

In the paper

“However, the relationship between these genes, the cellular processes in which they are involved, and the tissue structure as a whole remains poorly understood.”

In the paper

“CCL18 is also known to be involved in the recruitment and activation of CD4+ and CD8+ T cells and, more remarkably, is credited with playing a central role in perpetuating fibrotic processes through its involvement in a positive feedback loop that links activated macrophages to fibroblasts [26].”

What the sources say

• Not checked yetcites [26] Prasse A, Pechkovsky DV, Toews GB, Jungraithmayr W, Kollert F, Goldmann T, Vollmer E, Muller-Quernheim J, Zissel G: A vicious circle of alveolar macrophages and fibroblasts perpetuates pulmonary fibrosis via CCL18. Am J Respir Crit Care Med. 2006, 173: 781-792. 10.1164/rccm.200509-1518OC. source

In the paper

“Co-expressed with Mac-1 components, the hypoxia-inducible factor 1 (HIF1A) is a well characterized transcription factor that performs an essential role in cellular responses to hypoxia. HIF1A is also involved in the regulation of macrophage migration, and modulates the metabolism of immune cells exposed to low oxygen tensions in hypoxic areas of inflamed tissues [30].”

What the sources say

• Not checked yetcites [30] Sitkovsky M, Lukashev D: Regulation of immune cells by local-tissue oxygen tension: HIF1 alpha and adenosine receptors. Nat Rev Immunol. 2005, 5: 712-721. 10.1038/nri1685. source

In the paper

“We have shown previously that weight loss is associated with improvement in the inflammatory profile, together with regression of macrophage infiltration in WAT [11].”

What the sources say

• Not checked yetcites [11] Clement K, Viguerie N, Poitou C, Carette C, Pelloux V, Curat CA, Sicard A, Rome S, Benis A, Zucker JD, Vidal H, Laville M, Barsh GS, Basdevant A, Štich V, Stich V, Cancello R, Langin D: Weight loss regulates inflammation-related genes in white adipose tissue of obese subjects. FASEB J. 2004, 18: 1657-1669. 10.1096/fj.04-2204com. source

In the paper

“Available data demonstrate that the synthesis of CCL18 by alternatively activated macrophages is induced by Th2 cytokines, integrin beta 2 (ITGB2) and the scavenger receptor (CD163) [26].”

What the sources say

• Not checked yetcites [26] Prasse A, Pechkovsky DV, Toews GB, Jungraithmayr W, Kollert F, Goldmann T, Vollmer E, Muller-Quernheim J, Zissel G: A vicious circle of alveolar macrophages and fibroblasts perpetuates pulmonary fibrosis via CCL18. Am J Respir Crit Care Med. 2006, 173: 781-792. 10.1164/rccm.200509-1518OC. source

In the paper

“Elevated inflammatory proteins in obese individuals [1] suggest that inflammation may play a determinant role in connecting obesity to metabolic, hepatic and cardiovascular diseases [2], and to some cancers [3].”

What the sources say

• Not checked yetcites [1] Ridker PM, Buring JE, Cook NR, Rifai N: C-reactive protein, the metabolic syndrome, and risk of incident cardiovascular events: an 8-year follow-up of 14 719 initially healthy American women. Circulation. 2003, 107: 391-397. 10.1161/01.CIR.0000055014.62083.05. source
• Not checked yetcites [2] Hotamisligil GS: Inflammation and metabolic disorders. Nature. 2006, 444: 860-867. 10.1038/nature05485. source
• Not checked yetcites [3] Hursting SD, Nunez NP, Varticovski L, Vinson C: The obesity-cancer link: lessons learned from a fatless mouse. Cancer Res. 2007, 67: 2391-2393. 10.1158/0008-5472.CAN-06-4237. source

In the paper

“However, in spite of substantial evidence demonstrating the existence of a low-grade inflammatory component in obesity [5], the molecular mechanisms that link inflammatory changes to the development, aggravation, maintenance, and resistance to treatment that characterize obesity states remain poorly understood.”

What the sources say

• Not checked yetcites [5] Cottam DR, Mattar SG, Barinas-Mitchell E, Eid G, Kuller L, Kelley DE, Schauer PR: The chronic inflammatory hypothesis for the morbidity associated with morbid obesity: implications and effects of weight loss. Obes Surg. 2004, 14: 589-600. 10.1381/096089204323093345. source

In the paper

“In obese human subjects, large-scale transcriptomic analyses of WAT, in stable weight conditions or during weight loss, led mostly to the description of inflammatory changes and produced extensive lists of regulated genes involved in a number of biological functions [14].”

What the sources say

• Not checked yetcites [14] Viguerie N, Poitou C, Cancello R, Stich V, Clement K, Langin D: Transcriptomics applied to obesity and caloric restriction. Biochimie. 2005, 87: 117-123. 10.1016/j.biochi.2004.12.011. source

In the paper

“suggest that the phenotypic changes in human pre-adipocytes, induced by a pro-inflammatory environment, are associated with excessive synthesis of ECM components, which may contribute to tissue deterioration.”

In the paper

“Although some molecules secreted by WAT, such as leptin and adiponectin, are synthesized by mature adipocytes [8], the non-adipose SVF, comprising infiltrated macrophages among other cellular types, is a source of inflammation-related molecules that may exert a local action on adipose tissue biology, particularly within the enlarged WAT [9-11].”

What the sources say

• Not checked yetcites [9] Xu H, Barnes GT, Yang Q, Tan G, Yang D, Chou CJ, Sole J, Nichols A, Ross JS, Tartaglia LA, Chen H: Chronic inflammation in fat plays a crucial role in the development of obesity-related insulin resistance. J Clin Invest. 2003, 112: 1821-1830. 10.1172/JCI200319451. source
• Not checked yetcites [10] Curat CA, Miranville A, Sengenes C, Diehl M, Tonus C, Busse R, Bouloumie A: From blood monocytes to adipose tissue-resident macrophages: induction of diapedesis by human mature adipocytes. Diabetes. 2004, 53: 1285-1292. 10.2337/diabetes.53.5.1285. source
• Not checked yetcites [11] Clement K, Viguerie N, Poitou C, Carette C, Pelloux V, Curat CA, Sicard A, Rome S, Benis A, Zucker JD, Vidal H, Laville M, Barsh GS, Basdevant A, Štich V, Stich V, Cancello R, Langin D: Weight loss regulates inflammation-related genes in white adipose tissue of obese subjects. FASEB J. 2004, 18: 1657-1669. 10.1096/fj.04-2204com. source

In the paper

“White adipose tissue (WAT), now considered as a pivotal endocrine organ, contributes to the systemic inflammation by producing biomolecules, including pro-inflammatory mediators, whose estimated number grows constantly and whose synthesis is altered along with the expansion of the adipose tissue [6,7].”

What the sources say

• Not checked yetcites [6] Ailhaud G: Adipose tissue as an endocrine organ. Int J Obes Relat Metab Disord. 2000, 24 (Suppl 2): S1-3. source
• Not checked yetcites [7] Lyon CJ, Law RE, Hsueh WA: Minireview: adiposity, inflammation, and atherogenesis. Endocrinology. 2003, 144: 2195-2200. 10.1210/en.2003-0285. source

In the paper

“Recent data provided by our team showed that human pre-adipocytes in contact with activated macrophage media display a fibroblastic-like appearance, significantly proliferate and acquire pro-inflammatory properties [42].”

What the sources say

• Not checked yetcites [42] Lacasa D, Taleb S, Keophiphath M, Miranville A, Clement K: Macrophage-secreted factors impair human adipogenesis: involvement of pro-inflammatory state in pre-adipocytes. Endocrinology. 2007, 148: 868-877. 10.1210/en.2006-0687. source

In the paper

“Our study of functional profiles and transcriptomic interactions characterizing the adipose tissue of subjects in the obese static phase confirm the strong relationship linking inflammatory processes and ECM remodeling, associated with different inflammatory cell types and to some degree of interstitial fibrosis in WAT.”

In the paper

“A relationship between lymphocyte count and the weight of visceral and subcutaneous fat pads was also noted [48].”

What the sources say

• Not checked yetcites [48] Caspar-Bauguil S, Cousin B, Andre M, Nibbelink M, Galinier A, Periquet B, Casteilla L, Penicaud L: Weight-dependent changes of immune system in adipose tissue: importance of leptin. Exp Cell Res. 2006, 312: 2195-2202. 10.1016/j.yexcr.2006.03.023. source

In the paper

“In obese mice, a shift in the activation state of WAT macrophages from an M2 'alternatively activated' state to an M1 'pro-inflammatory state' was observed in response to diet-induced obesity [47].”

What the sources say

• Not checked yetcites [47] Lumeng CN, Bodzin JL, Saltiel AR: Obesity induces a phenotypic switch in adipose tissue macrophage polarization. J Clin Invest. 2007, 117: 175-184. 10.1172/JCI29881. source

In the paper

“To date, only a few comparative studies have described the lymphoid accumulation in WAT of obese subjects [49].”

What the sources say

• Not checked yetcites [49] Marti A, Marcos A, Martinez JA: Obesity and immune function relationships. Obes Rev. 2001, 2: 131-140. 10.1046/j.1467-789x.2001.00025.x. source

In the paper

“From a temporal perspective, human obesity can be considered as a set of phenotypes that develop successively over time. In this sequence one can distinguish: a 'pre-obese static phase' when the individual at risk of obesity has a stable weight and energy balance status; a 'dynamic weight gain phase' during which weight increases as a result of a positive energy balance with intakes exceeding”

What the sources say

• Not checked yetcites [60] Obesity: Preventing and Managing the Global Epidemic. Report of a WHO Consultation. World Health Organ Tech Rep Ser. 2000, 894: i-xii. 1-253.

In the paper

“In fibrotic diseases it has been shown that the accumulation of ECM components can be driven primarily by inflammatory processes [59].”

What the sources say

• Not checked yetcites [59] Iredale JP: Models of liver fibrosis: exploring the dynamic nature of inflammation and repair in a solid organ. J Clin Invest. 2007, 117: 539-548. 10.1172/JCI30542. source

In the paper

“The co-expression network analysis showed a concomitant up-regulation of genes related to both matrix metalloproteinase and tissue inhibitor of metalloproteinase families (online supplementary Table 2 [20]), which could explain the reduced degradation of ECM components after weight loss.”

What the sources say

• Not checked yetcites [20] Companion Website to this Study. [http://corneliu.henegar.info/projects/FunNet/genome_biol_2008/index.htm]

In the paper

“This may be associated with the presence of M1 macrophages, since genes encoding pro-inflammatory factors were also induced.”

In the paper

“Examination of the functional interaction networks indicated that a similar phenomenon may occur in the obese WAT, involving the presence of inflammatory cells and a possible contribution by fibroblast derived pre-adipocytes in producing ECM components.”

In the paper

“In the initial phase, behavioral and environmental factors could play a key role in the constitution of adipose tissue excess on a genetically predisposed background [61].”

What the sources say

• Not checked yetcites [61] Mutch DM, Clement K: Unraveling the genetics of human obesity. PLoS Genet. 2006, 2: e188-10.1371/journal.pgen.0020188. source

In the paper

“Both our functional analysis and cellular studies indicate that such a pathological process might occur in obese WAT.”

In the paper

“Our full-scale exploratory analysis of the obese WAT transcriptomic signature highlights the central place occupied by inflammatory and immune processes and shows the strong interaction with ECM components grouped in the same module (module 1).”

In the paper

“However, these results do not exclude the role of mature adipocytes in the excessive synthesis of some ECM components.”

In the paper

“Fibrosis may be more than a passive witness of the pathologic state of the tissue, possibly indicating a degree of irreversibility in the evolution of obesity, as seems to be suggested by its persistence after a drastic decrease of the adipose mass, in spite of the regression of the local inflammatory phenomena.”

In the paper

“Major histopathological features were recorded and semi-quantified according to previously published criteria [80].”

What the sources say

• Not checked yetcites [80] Kleiner DE, Brunt EM, Van Natta M, Behling C, Contos MJ, Cummings OW, Ferrell LD, Liu YC, Torbenson MS, Unalp-Arida A, Yeh M, McCullough AJ, Sanyal AJ, Nonalcoholic Steatohepatitis Clinical Research Network: Design and validation of a histological scoring system for nonalcoholic fatty liver disease. Hepatology. 2005, 41: 1313-1321. 10.1002/hep.20701. source

In the paper

“We validated the gene expression changes by reverse transcription and RTqPCR, performed as described in [63].”

What the sources say

• Not checked yetcites [63] Clement K, Viguerie N, Diehn M, Alizadeh A, Barbe P, Thalamas C, Storey JD, Brown PO, Barsh GS, Langin D: In vivo regulation of human skeletal muscle gene expression by thyroid hormone. Genome Res. 2002, 12: 281-291. 10.1101/gr.207702. source

In the paper

“Slides were coded and analyzed by a single expert pathologist blind to the identity of the biopsy.”

In the paper

“Thin sections (5 μm thick) were haematoxylin-eosin stained and analyzed by three independent observers in a blind fashion with a Zeiss 20 Axiostar Plus microscope (Zeiss, Germany).”

In the paper

“Several quality cross-checks (for total RNA quality, aRNA quality, dye incorporation efficiency, and so on) and microarray 'dye swap' experiments were also performed.”

In the paper

“EntrezGene numbers [72] were used as a standard transcript accession system to ensure a correct over-representation analysis, as they allow one to map gene identifiers to GO or KEGG biological categories.”

What the sources say

• Not checked yetcites [72] Maglott D, Ostell J, Pruitt KD, Tatusova T: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Res. 2007, 35: D26-31. 10.1093/nar/gkl993. source

In the paper

“There was no significant difference in terms of age between obese subjects and lean controls.”

In the paper

“All clinical investigations were performed according to the Declaration of Helsinki and were approved by the Ethics Committees of Hôtel-Dieu hospital (Paris, France).”

In the paper

“Regardless of the actual mechanism explaining its persistence, the increase of interstitial fibrosis in the adipose tissue could impair cell-cell contact and, therefore, interfere with cellular signaling mechanisms that regulate adipogenesis and metabolic functions of WAT.”

In the paper

“The resulting p values were adjusted for multiple testing errors by applying the Storey (2002) FDR correction approach [68].”

What the sources say

• Not checked yetcites [68] Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci USA. 2003, 100: 9440-9445. 10.1073/pnas.1530509100. source

In the paper

“A print-tip loess normalization of the microarray experiments was performed after the log-transformation of the background-corrected expression measurements, as indicated in [67].”

What the sources say

• Not checked yetcites [67] Smyth GK, Speed T: Normalization of cDNA microarray data. Methods. 2003, 31: 265-273. 10.1016/S1046-2023(03)00155-5. source

In the paper

“This threshold parameter, which represents a co-expression significance indicator, was determined by maximizing a scale-free topology criterion as previously described [78].”

What the sources say

• Not checked yetcites [78] Zhang B, Horvath S: A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005, 4: Article 17-Epub 2005 source

In the paper

“Significant differential expression was established by imposing a 5% FDR threshold in the SAM selection procedure for all conditions.”

What the sources say

• Not checked yetcites [21] Tusher VG, Tibshirani R, Chu G: Significance analysis of microarrays applied to the ionizing radiation response. Proc Natl Acad Sci USA. 2001, 98: 5116-5121. 10.1073/pnas.091062498. source

In the paper

“After washing in phosphate-buffered saline (PBS), the SVF cells were suspended in DMEM-10% fetal bovine serum and used for cell culture at passage 2 to eliminate non-pre-adipocyte cell contamination as confirmed by negative staining for macrophage markers (Ham 56 and Mac-1).”

In the paper

“In all analyses the threshold for statistical significance was considered as corresponding to a p value < 0.05.”

In the paper

“We used 18S ribosomal RNA (Ribosomal RNA Control TaqMan Assay kit, Applied Biosystems, Foster City, CA, USA) as a normalization control.”

In the paper

“In all conditions in which multiple testing errors were expected, due to the high number of consecutive statistical computations, the p values computed from the aforementioned tests were adjusted by applying the Storey (2002) correction approach [68], corresponding to an estimated FDR of 5%.”

What the sources say

• Not checked yetcites [68] Storey JD, Tibshirani R: Statistical significance for genomewide studies. Proc Natl Acad Sci USA. 2003, 100: 9440-9445. 10.1073/pnas.1530509100. source

In the paper

“Signed informed consents were obtained for all subjects involved in the study.”

In the paper

“It cannot be excluded that this enzymatic digestion technique may have a potential influence on the expression profiles of separated cells, as noted previously in mouse studies [65].”

What the sources say

• Not checked yetcites [65] Ruan H, Zarnowski MJ, Cushman SW, Lodish HF: Standard isolation of primary adipose cells from mouse epididymal fat pads induces inflammatory mediators and down-regulates adipocyte genes. J Biol Chem. 2003, 278: 47585-47593. 10.1074/jbc.M305257200. source

In the paper

“After expert inspection of automated annotation results, the fourth information-specific level of GO was retained for further analysis, as it provided an optimal trade-off between the specificity of the annotating information and its biological interpretability.”