TNFa has been proposed as a link between metabolic dysregulation and inflammation and/or vascular dysfunction in diabetes, and it is well established as a key molecule in diabetic retinopathy

April 1, 2017

1 | Volume 6 | Issue 2 | e14672 Estrogen-Dependent Genes Bioinformatic analysis and downstream annotation E-dependent DEG were ranked according to the methods described in the results section. Specific methods for Gene Ontology, GeneGo pathways analysis and Dragon estrogen response element Finder version 6 are detailed below. 1. Gene Ontology Analysis. E-dependent DEG lists were annotated according to the GO database using ontology categories for Molecular Function, Cellular Component and Biological Processes. The representation of E-dependent DEG within each ontology category was measured and statistical significance of the overlap was done using a hypergeometric p-value without multiple testing corrections, to determine the likelihood of coincidental overlap with ontology groups. A p-value lower than 0.05 indicates over representation of genes from the E-dependent DEG list within that particular category, suggestive of a functional effect. Annotation of the E-dependent DEG lists using 7329399 GO was conducted by the AGRF Melbourne, Australia. 2. Dragon ERE Locator version 6. Nucleotide search from National Center for Biotechnology Information was used to retrieve the sequence information of the differentially expressed genes within the selected Biological Processes categories in the FASTA format. These sequences were then examined for the presence of ERE binding sites using the Erythromycin Cyclocarbonate latest Dragon ERE Finder version 6.0 based upon information present in the transcriptional regulation, from patterns to profiles database. The detection algorithm was tested on several large datasets and achieved a sensitivity of 83%. An ERE is defined as a site which contains the 17 basepairs consensus sequence with its flanking 20 nucleotides on either side against the promoter sequences of Eukaryotic Promoter Database . 3. GeneGo pathway analysis. The E-dependent DEG list containing the 450 unique E-dependent DEG, complete with Illumina transcript identifiers, were uploaded from a Microsoft Excel spreadsheet onto Metacore 5.0 software . GeneGo recognizes the Illumina identifiers and maps the E-dependent DEG to the MetaCoreTM data 2187993 analysis suite, generating maps to describe common pathways or molecular connections between Edependent DEG on the list. Graphical representations of the molecular relationships between genes were generated using the GeneGo pathway analysis, based upon processes showing significant association. Results E-dependent Differentially expressed genes in ArKO compared to WTs Microarray analysis of whole genome expression in ArKO ovary compared to WT ovary identified 450 differentially expressed transcripts with a 62-fold expression difference that was significant . This list is referred to as the E-dependent DEG list and can be found in full in the supplementary data. The 450 E-dependent DEGs represent,0.94% of the total number of transcripts present on the Illumina BeadChip. Of these 450 E-dependent DEG, 291 were up regulated, and 159 DEG Genbank 1 2 3 4 5 6 7 8 NM_178396 NM_008491 XM_130383 XM_485085 NM_011413 XM_355911 NM_008770 XM_357518 Gene symbol Car12 Lcn2 8030411F24Rik Defb36 C4 mediates alcohol-induced downregulation of intestinal tight junction proteins. Am J Physiol Gastrointest Liver Physiol 299: G64351. Raftopoulou M, Etienne-Manneville S, Self A, Nicholls S, Hall A Regulation of cell migration by the C2 domain of the tumor suppressor PTEN. Science 303: 1179181. 65. Dey N, Crosswell HE, De P, Parsons R, Peng Q, et al. The protein pho