Sitras V, Fenton C, Paulssen R, Vårtun A, Acharya G. Differences in Gene Expression between First and Third Trimester Human Placenta: A Microarray Study. PLoS ONE. 2012; 7(3):33294.
Article
Google Scholar
Winn VD, Haimov-Kochman R, Paquet AC, Yang YJ, Madhusudhan MS, Gormley M, Feng K-TV, Bernlohr DA, McDonagh S, Pereira L, Sali A, Fisher SJ. Gene expression profiling of the human maternal-fetal interface reveals dramatic changes between midgestation and term. Endocrinology. 2007; 148(3):1059–1079.
Article
CAS
PubMed
Google Scholar
Mikheev AM, Nabekura T, Kaddoumi A, Bammler TK, Govindarajan R, Hebert MF, Unadkat JD. Profiling gene expression in human placentae of different gestational ages: an OPRU Network and UW SCOR Study. Reprod Sci. 2008; 15(9):866–77. doi:10.1177/1933719108322425.
Article
CAS
PubMed
PubMed Central
Google Scholar
Uusküla L, Männik J, Rull K, Minajeva A, Kõks S, Vaas P, Teesalu P, Reimand J, Laan M. Mid-gestational gene expression profile in placenta and link to pregnancy complications. PloS ONE. 2012; 7(11):49248. doi:10.1371/journal.pone.0049248.
Article
Google Scholar
Kleinrouweler CE, van Uitert M, Moerland PD, Ris-Stalpers C, van der Post JAM, Afink GB. Differentially expressed genes in the pre-eclamptic placenta: a systematic review and meta-analysis. PLoS ONE. 2013; 8(7):68991.
Article
Google Scholar
Sõber S, Reiman M, Kikas T, Rull K, Inno R, Vaas P, Teesalu P, Marti JML, Mattila P, Laan M. Extensive shift in placental transcriptome profile in preeclampsia and placental origin of adverse pregnancy outcomes. Sci Rep. 2015; 5:13336. doi:10.1038/srep13336.
Article
PubMed
PubMed Central
Google Scholar
Vaiman D, Calicchio R, Miralles F. Landscape of transcriptional deregulations in the preeclamptic placenta. PloS ONE. 2013; 8(6):65498. doi:10.1371/journal.pone.0065498.
Article
Google Scholar
Moslehi R, Ambroggio X, Nagarajan V, Kumar A, Dzutsev A. Nucleotide excision repair/transcription gene defects in the fetus and impaired TFIIH-mediated function in transcription in placenta leading to preeclampsia. BMC genomics. 2014; 15(1):373. doi:10.1186/1471-2164-15-373.
Article
PubMed
PubMed Central
Google Scholar
Kaartokallio T, Cervera A, Kyllönen A, Laivuori K. Gene expression profiling of pre-eclamptic placentae by RNA sequencing. Sci Rep. 2015; 5:14107. doi:10.1038/srep14107.
Article
CAS
PubMed
PubMed Central
Google Scholar
Founds SA, Conley YP, Lyons-Weiler JF, Jeyabalan A, Allen Hogge W, Conrad KP. Altered global gene expression in first trimester placentas of women destined to develop preeclampsia. Placenta. 2009; 30(1):15–24.
Article
CAS
PubMed
Google Scholar
Saben J, Zhong Y, McKelvey S, Dajani NK, Andres A, Badger TM, Gomez-Acevedo H, Shankar K. A comprehensive analysis of the human placenta transcriptome. Placenta. 2014; 35(2):125–31.
Article
CAS
PubMed
Google Scholar
Kim J, Zhao K, Jiang P, Lu ZX, Wang J, Murray JC, Xing Y. Transcriptome landscape of the human placenta. BMC Genomics. 2012; 13(1):115.
Article
CAS
PubMed
PubMed Central
Google Scholar
Langfelder P, Castellani LW, Zhou Z, Paul E, Davis R, Schadt EE, Lusis AJ, Horvath S, Mehrabian M. A systems genetic analysis of high density lipoprotein metabolism and network preservation across mouse models. Biochim Biophys Acta. 2012; 1821(3):435–47.
Article
CAS
PubMed
Google Scholar
Hu Y, Wu G, Rusch M, Lukes L, Buetow KH, Zhang J, Hunter KW. Integrated cross-species transcriptional network analysis of metastatic susceptibility. Proc Natl Acad Sci USA. 2012; 109(8):3184–189.
Article
CAS
PubMed
PubMed Central
Google Scholar
Voineagu I, Wang X, Johnston P, Lowe JK, Tian Y, Horvath S, Mill J, Cantor RM, Blencowe BJ, Geschwind DH. Transcriptomic analysis of autistic brain reveals convergent molecular pathology. Nature. 2011; 474(7351):380–4.
Article
CAS
PubMed
PubMed Central
Google Scholar
Oldham MC, Konopka G, Iwamoto K, Langfelder P, Kato T, Horvath S, Geschwind DH. Functional organization of the transcriptome in human brain. Nat Neurosci. 2008; 11(11):1271–1282.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gupta S, Ellis SE, Ashar FN, Moes A, Bader JS, Zhan J, West AB, Arking DE. Transcriptome analysis reveals dysregulation of innate immune response genes and neuronal activity-dependent genes in autism. Nat Commun. 2014; 5:5748.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xue Z, Huang K, Cai C, Cai L, Jiang C-y, Feng Y, Liu Z, Zeng Q, Cheng L, Sun YE, Liu J-y, Horvath S, Fan G. Genetic programs in human and mouse early embryos revealed by single-cell RNA sequencing. Nature. 2013; 500(7464):593–7.
Article
CAS
PubMed
PubMed Central
Google Scholar
Langfelder P, Horvath S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics. 2008; 9:559.
Article
PubMed
PubMed Central
Google Scholar
Langfelder P, Zhang B, Horvath S. Defining clusters from a hierarchical cluster tree: the Dynamic Tree Cut package for R. Bioinformatics. 2008; 24(5):719–20.
Article
CAS
PubMed
Google Scholar
Lee KJ, Shim SH, Kang KM, Kang JH, Park DY, Kim SH, Farina A, Shim SS, Cha DH. Global gene expression changes induced in the human placenta during labor. Placenta. 2010; 31(8):698–704.
Article
PubMed
Google Scholar
Langfelder P, Luo R, Oldham MC, Horvath S. Is my network module preserved and reproducible?PLoS Comput Biol. 2011; 7(1):1001057.
Article
Google Scholar
Gude NM, Roberts CT, Kalionis B, King RG. Growth and function of the normal human placenta. Thromb Res. 2004; 114(5-6):397–407.
Article
CAS
PubMed
Google Scholar
Finn EH, Smith CL, Rodriguez J, Sidow A, Baker JC. Maternal Bias and Escape from X Chromosome Imprinting in the Midgestation Mouse Placenta. Dev Biol. 2014; 390(1):80–92.
Article
CAS
PubMed
PubMed Central
Google Scholar
Harder L, Puller AC, Horstmann MA. ZNF423: Transcriptional modulation in development and cancer. Mol Cell Oncol. 2014; 1(3):969655.
Article
Google Scholar
Harder L, Eschenburg G, Zech A, Kriebitzsch N, Otto B, Streichert T, Behlich AS, Dierck K, Klingler B, Hansen A, Stanulla M, Zimmermann M, Kremmer E, Stocking C, Horstmann MA. Aberrant ZNF423 impedes B cell differentiation and is linked to adverse outcome of ETV6-RUNX1 negative B precursor acute lymphoblastic leukemia. J Exp Med. 2013; 210(11):2289–304.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tsai RY, Reed RR. Identification of DNA recognition sequences and protein interaction domains of the multiple-Zn-finger protein Roaz. Mol Cell Biol. 1998; 18(11):6447–456.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang MM, Reed RR. Molecular cloning of the olfactory neuronal transcription factor Olf-1 by genetic selection in yeast. Nature. 1993; 364(6433):121–6.
Article
CAS
PubMed
Google Scholar
Khong TY, De Wolf F, Robertson WB, Brosens I. Inadequate maternal vascular response to placentation in pregnancies complicated by pre-eclampsia and by small-for-gestational age infants. Br J Obstet Gynaecol. 1986; 93(10):1049–1059.
Article
CAS
PubMed
Google Scholar
Kim YM, Bujold E, Chaiworapongsa T, Gomez R, Yoon BH, Thaler HT, Rotmensch S, Romero R. Failure of physiologic transformation of the spiral arteries in patients with preterm labor and intact membranes. Am J Obstet Gynaecol. 2003; 189(4):1063–1069.
Article
Google Scholar
Kim YM, Chaiworapongsa T, Gomez R, Bujold E, Yoon BH, Rotmensch S, Thaler HT, Romero R. Failure of physiologic transformation of the spiral arteries in the placental bed in preterm premature rupture of membranes. Am J Obstet Gynaecol. 2002; 187(5):1137–1142.
Article
Google Scholar
Uzun A, Laliberte A, Parker J, Andrew C, Winterrowd E, Sharma S, Istrail S, Padbury JF. dbPTB: a database for preterm birth. Database. 2012; 2012(0):069–069.
Article
Google Scholar
Blair JD, Yuen RKC, Lim BK, McFadden DE, von Dadelszen P, Robinson WP. Widespread DNA hypomethylation at gene enhancer regions in placentas associated with early-onset pre-eclampsia. Mol Hum Reprod. 2013; 19(10):697–708.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wu D, Lim E, Vaillant F, Asselin-Labat ML, Visvader JE, Smyth GK. ROAST: rotation gene set tests for complex microarray experiments. Bioinformatics. 2010; 26(17):2176–182.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lehman A, Stittrich AB, Glusman G, Zong Z, Li H, Eydoux P, Senger C, Lyons C, Roach JC, Patel M. Diffuse angiopathy in Adams-Oliver syndrome associated with truncating DOCK6 mutations. Am J Med Genet. 2014; 164A(10):2656–662.
Article
PubMed
Google Scholar
Sitras V, Paulssen R, Leirvik J, Vårtun A, Acharya G. Placental gene expression profile in intrauterine growth restriction due to placental insufficiency. Reprod Sci. 2009; 16(7):701–11.
Article
CAS
PubMed
Google Scholar
Løset M, Mundal SB, Johnson MP, Fenstad MH, Freed KA, Lian IA, Eide IP, Bjørge L, Blangero J, Moses EK, Austgulen R. A transcriptional profile of the decidua in preeclampsia. Am J Obstet Gynaecol. 2011; 204(1):84–127.
Article
Google Scholar
Cheng LE, Zhang J, Reed RR. The transcription factor Zfp423/OAZ is required for cerebellar development and CNS midline patterning. Dev Biol. 2007; 307(1):43–52.
Article
CAS
PubMed
PubMed Central
Google Scholar
Liao D. Emerging Roles of the EBF Family of Transcription Factors in Tumor Suppression. Mol Cancer Res. 2009; 7(12):1893–901.
Article
CAS
PubMed
Google Scholar
Redman CW, Sargent IL. Latest advances in understanding preeclampsia. Science. 2005; 308(5728):1592–1594.
Article
CAS
PubMed
Google Scholar
Tejera E, Bernardes Jao, Rebelo I. Preeclampsia: a bioinformatics approach through protein-protein interaction networks analysis. BMC Syst Biol. 2012; 6(1):97.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tejera E, Bernardes Jao, Rebelo I. Co-expression network analysis and genetic algorithms for gene prioritization in preeclampsia. BMC Med Genomics. 2013; 6(1):51.
Article
PubMed
PubMed Central
Google Scholar
Brancati F, Fortugno P, Bottillo I, Lopez M, Josselin E, Boudghene-Stambouli O, Agolini E, Bernardini L, Bellacchio E, Iannicelli M, Rossi A, Dib-Lachachi A, Stuppia L, Palka G, Mundlos S, Stricker S, Kornak U, Zambruno G, Dallapiccola B. Mutations in PVRL4, encoding cell adhesion molecule nectin-4, cause ectodermal dysplasia-syndactyly syndrome. Am J Hum Genet. 2010; 87(2):265–73.
Article
CAS
PubMed
PubMed Central
Google Scholar
Pavlova NN, Pallasch C, Elia AE, Braun CJ, Westbrook TF, Hemann M, Elledge SJ. A role for PVRL4-driven cell-cell interactions in tumorigenesis. Elife. 2013; 2:00358.
Article
Google Scholar
Derycke MS, Pambuccian SE, Gilks CB, Kalloger SE, Ghidouche A, Lopez M, Bliss RL, Geller MA, Argenta PA, Harrington KM, Skubitz APN. Nectin 4 overexpression in ovarian cancer tissues and serum: potential role as a serum biomarker. Am J Clin Pathol. 2010; 134(5):835–45.
Article
CAS
PubMed
PubMed Central
Google Scholar
McCowan LME, Roberts CT, Dekker GA, Taylor RS, Chan EHY, Kenny LC, Baker PN, Moss-Morris R, Chappell LC, North RA, SCOPE consortium. Risk factors for small-for-gestational-age infants by customised birthweight centiles: data from an international prospective cohort study. Br J Obstet Gynaecol. 2010; 117(13):1599–1607.
Article
CAS
Google Scholar
Lawrence M, Huber W, Pagès H, Aboyoun P, Carlson M, Gentleman R, Morgan MT, Carey VJ. Software for computing and annotating genomic ranges. PLoS Comput Biol. 2013; 9(8):1003118.
Article
Google Scholar
Law CW, Chen Y, Shi W, Smyth GK. Voom: precision weights unlock linear model analysis tools for RNA-seq read counts. Genome Biol. 2014; 15(2):29.
Article
Google Scholar
Zhang B, Horvath S. A general framework for weighted gene co-expression network analysis. Stat Appl Genet Mol Biol. 2005; 4:17.
Google Scholar
Irizarry RA, Bolstad BM, Collin F, Cope LM, Hobbs B, Speed TP. Summaries of Affymetrix GeneChip probe level data. Nucleic Acids Res. 2003; 31(4):15.
Article
Google Scholar
Falcon S, Gentleman R. Using GOstats to test gene lists for GO term association. Bioinformatics. 2007; 23(2):257–8.
Article
CAS
PubMed
Google Scholar
Kwon AT, Arenillas DJ, Hunt RW, Wasserman WW. oPOSSUM-3: Advanced Analysis of Regulatory Motif Over-Representation Across Genes or ChIP-Seq Datasets. G3. 2012; 2(Spetember):987–1002.
Article
CAS
PubMed
PubMed Central
Google Scholar
Mathelier A, Zhao X, Zhang AW, Parcy F, Worsley-Hunt R, Arenillas DJ, Buchman S, Chen Cy, Chou A, Ienasescu H, Lim J, Shyr C, Tan G, Zhou M, Lenhard B, Sandelin A, Wasserman WW. JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles. Nucleic Acids Res. 2013; 42:142–7.
Article
Google Scholar