CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes

Combinatorial interactions of sequence-specific trans-acting factors with localized genomic cis-element clusters are the principal mechanism for regulating tissue-specific and developmental gene expression. With the emergence of expanding numbers of genome-wide expression analyses, the identification of the cis-elements responsible for specific patterns of transcriptional regulation represents a critical area of investigation. Computational methods for the identification of functional cis-regulatory modules are difficult to devise, principally because of the short length and degenerate nature of individual cis-element binding sites and the inherent complexity that is generated by combinatorial interactions within cis-clusters. Filtering candidate cis-element clusters based on phylogenetic conservation is helpful for an individual ortholog gene pair, but combining data from cis-conservation and coordinate expression across multiple genes is a more difficult problem. To approach this, we have extended an ortholog gene-pair database with additional analytical architecture to allow for the analysis and identification of maximal numbers of compositionally similar and phylogenetically conserved cis-regulatory element clusters from a list of user-selected genes. The system has been successfully tested with a series of functionally related and microarray profile-based co-expressed ortholog pairs of promoters and genes using known regulatory regions as training sets and co-expressed genes in the olfactory and immunohematologic systems as test sets. CisMols Analyzer is accessible via a Web interface at

GenomeTrafac: a whole genome resource for the detection of transcription factor binding site clusters associated with conventional and microRNA encoding genes conserved between mouse and human gene orthologs

Transcriptional cis-regulatory control regions frequently are found within non-coding DNA segments conserved across multi-species gene orthologs. Adopting a systematic gene-centric pipeline approach, we report here the development of a web-accessible database resource—GenomeTraFac ()—that allows genome-wide detection and characterization of compositionally similar cis-clusters that occur in gene orthologs between any two genomes for both microRNA genes as well as conventional RNA-encoding genes. Each ortholog gene pair can be scanned to visualize overall conserved sequence regions, and within these, the relative density of conserved cis-element motif clusters form graph peak structures. The results of these analyses can be mined en masse to identify most frequently represented cis-motifs in a list of genes. The system also provides a method for rapid evaluation and visualization of gene model-consistency between orthologs, and facilitates consideration of the potential impact of sequence variation in conserved non-coding regions to impact complex cis-element structures. Using the mouse and human genomes via the NCBI Reference Sequence database and the Sanger Institute miRBase, the system demonstrated the ability to identify validated transcription factor targets within promoter and distal genomic regulatory regions of both conventional and microRNA genes

Shaping ability of waveone primary reciprocating files and oneshape rotary files in severely curved root canals: A comparative study with micro-computed tomography

Introduction: This study compared the amount of canal transportation, canal centering ability after instrumentation and time required for shaping of canal with WaveOne Primary Reciprocating file and OneShape Rotary file. Method: Thirty intact mesial roots of mandibular first molars were divided into Group I and Group II. Specimens in Group I were shaped with WaveOne Primary reciprocating files to the working length (WL) and specimens in Group II were shaped with OneShape Rotary file to the WL. Time required to prepare each canal was recorded. All the specimens were submitted to micro-computed tomography (µCT) unit for Pre- and post-instrumentation scan. Images were reconstructed and cross-sections corresponding to distances 3, 6 and 9 mm from the anatomic apex were selected for analysis. Statistical analysis was performed with Kruskal Wallis and paired t test. Results: Overall, both rotary files maintained root canal curvatures well. During canal preparation, OneShape file performed significantly better in the apical third when compared to the WaveOne Reciprocating file. WaveOne file required reasonably less time to prepare canal when rather than OneShape file

Shaping Ability of Waveone Primary Reciprocating Files and Oneshape Rotary Files in Severely Curved Root Canals: A Comparative Study with Micro-computed Tomography

Introduction: This study compared the amount of canal transportation, canal centering ability after instrumentation and time required for shaping of canal with WaveOne Primary Reciprocating file and OneShape Rotary file. Method: Thirty intact mesial roots of mandibular first molars were divided into Group I and Group II. Specimens in Group I were shaped with WaveOne Primary reciprocating files to the working length (WL) and specimens in Group II were shaped with OneShape Rotary file to the WL. Time required to prepare each canal was recorded. All the specimens were submitted to micro-computed tomography (µCT) unit for Pre- and post-instrumentation scan. Images were reconstructed and cross-sections corresponding to distances 3, 6 and 9 mm from the anatomic apex were selected for analysis. Statistical analysis was performed with Kruskal Wallis and paired t test. Results: Overall, both rotary files maintained root canal curvatures well. During canal preparation, OneShape file performed significantly better in the apical third when compared to the WaveOne Reciprocating file. WaveOne file required reasonably less time to prepare canal when rather than OneShape file