The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Piotr Zielenkiewicz - One of the best experts on this subject based on the ideXlab platform.
-
Overrepresentation of interactions between homologous proteins in interactomes
FEBS Letters, 2007Co-Authors: Jerzy Orlowski, Szymon Kaczanowski, Piotr ZielenkiewiczAbstract:It is well proved that the probability that a protein interacts with itself is higher than that it interacts with another protein. It has been recently shown that the probability of interaction is also higher for proteins with significant sequence similarity. In this paper we show that proteins sharing identical PFAM domains interact more often than expected by chance in Saccharomyces cerevisiae and Escherichia coli. We also analyze the variety of domain interfaces used by homologous proteins to interact and show that the Overrepresentation of interactions between homological proteins is not caused by small number of pairs of identical "sticky domains" shared between interacting proteins.
Vessela N Kristensen - One of the best experts on this subject based on the ideXlab platform.
-
Overrepresentation of transcription factor families in the genesets underlying breast cancer subtypes
BMC Genomics, 2012Co-Authors: Himanshu Joshi, Silje Nord, Arnoldo Frigessi, Anne Lise Borresendale, Vessela N KristensenAbstract:The human genome contains a large amount of cis-regulatory DNA elements responsible for directing both spatial and temporal gene-expression patterns. Previous studies have shown that based on their mRNA expression breast tumors could be divided into five subgroups (Luminal A, Luminal B, Basal, ErbB2+ and Normal-like), each with a distinct molecular portrait. Whole genome gene expression analysis of independent sets of breast tumors reveals repeatedly the robustness of this classification. Furthermore, breast tumors carrying a TP53 mutation show a distinct gene expression profile, which is in strong association to the distinct molecular portraits. The mRNA expression of 552 genes, which varied considerably among the different tumors, but little between two samples of the same tumor, has been shown to be sufficient to separate these tumor subgroups. We analyzed in silico the transcriptional regulation of genes defining the subgroups at 3 different levels: 1. We studied the pathways in which the genes distinguishing the subgroups of breast cancer may be jointly involved including upstream regulators (1st and 2nd level of regulation) as well as downstream targets of these genes. 2. Then we analyzed the promoter areas of these genes (−500 bp to +100 bp relative to the transcription start site) for canonical transcription binding sites using Genomatix. 3. We looked for the actual expression levels of the identified TF and how they correlate with the Overrepresentation of their TF binding sites in the separate groups. We report that promoter composition of the genes that most strongly predict the patient subgroups is distinct. The class-predictive genes showed a clearly different degree of Overrepresentation of transcription factor families in their promoter sequences. The study suggests that transcription factors responsible for the observed expression pattern in breast cancers may lead us to important biological pathways.
Paolo Cossurocca - One of the best experts on this subject based on the ideXlab platform.
-
chromosome 12p abnormalities in dysgerminoma of the ovary a fish analysis
Modern Pathology, 2006Co-Authors: Fadi Abdul W Karim, Robert E. Emerson, Helen Michael, Paolo Cossurocca, Shaobo Zhang, Lawrence M Roth, Wenxin Zheng, John N Eble, Timothy D JonesAbstract:Dysgerminoma is the most common malignant ovarian germ cell tumor and shares histological and immunophenotypical features with its testicular counterpart, seminoma. Chromosome 12p abnormalities are genetic hallmarks of testicular seminomas. Little is known about these genetic changes in dysgerminoma. We performed dual color fluorescence in situ hybridization (FISH) analyses with a centromeric α-satellite probe for chromosome 12 and a subtelomeric probe for 12p on paraffin-embedded tissue sections from 21 dysgerminomas and two gonadoblastomas. Chromosome 12p abnormalities were detected in 81% of dysgerminomas. In all, 57% of cases had only isochromosome 12p and 5% had only 12p Overrepresentation. In all, 19% had both isochrome 12p and 12p Overrepresentation. Gonadoblastomas were negative for isochromosome 12p or 12p Overrepresentation. Chromosome 12p abnormalities are common in dysgerminoma of the ovary. FISH analyses for chromosome 12p abnormalities may be a useful diagnostic adjunct for confirming the diagnosis of dysgerminoma and for distinguishing it from nongerm cell malignancies that enter into the differential diagnosis.
Donna Y Ford - One of the best experts on this subject based on the ideXlab platform.
-
historical and legal overview of special education Overrepresentation access and equity denied
Multiple Voices for Ethnically Diverse Exceptional Learners, 2016Co-Authors: Donna Y Ford, Charles J RussoAbstract:The history of the denial of equal education opportunities to Black children is a long one, whether through racial segregation or Overrepresentation in special education. No other group is as overreferred, overidentified, and overrepresented in special education as Black students, specifically Black males. The authors present an historical and legal overview of special education and critique in the 2015 report by Morgan, Farkas, Hillemeier, Mattison, Maczuga, Li, and Cook. Based on their analysis of limited criteria rather than comprehensive criteria, Morgan and colleagues claim that Blacks were not overrepresented in special education and that more should have been identified. This study created a swelter of discussion and debates that are not new but that the authors find to be biased, polemic, and deficit-oriented assertions. The potential impact of Morgan et al.'s work (arguments, findings, and conclusions) must be interrogated rather than discounted.
-
culturally different students in special education looking backward to move forward
Exceptional Children, 2012Co-Authors: Donna Y FordAbstract:As the “land of opportunity” and arguably the greatest country in the world, the United States continues to change—culturally, racially, and linguistically. Reports abound regarding the changing demographics of the country and its schools. Over a 2-decade span (1989–2009), the percentage of “minority” students in public schools (referring to Hispanic American, African American, Asian American, and Native American students) increased from 32% to 45%. This trend is expected to continue, with these 4 groups soon becoming the numerical majority nationally, as is the case already in many school districts. With these changes come growing pains. Special education often receives attention, including debates and litigation, regarding disproportionality or Overrepresentation, particularly among African American students (especially males). This albatross has plagued the field for decades. This article presents an overview of demographics in schools and special education, discusses Overrepresentation, and provides s...
Szymon Kaczanowski - One of the best experts on this subject based on the ideXlab platform.
-
Overrepresentation of interactions between homologous proteins in interactomes
FEBS Letters, 2007Co-Authors: Jerzy Orlowski, Szymon Kaczanowski, Piotr ZielenkiewiczAbstract:It is well proved that the probability that a protein interacts with itself is higher than that it interacts with another protein. It has been recently shown that the probability of interaction is also higher for proteins with significant sequence similarity. In this paper we show that proteins sharing identical PFAM domains interact more often than expected by chance in Saccharomyces cerevisiae and Escherichia coli. We also analyze the variety of domain interfaces used by homologous proteins to interact and show that the Overrepresentation of interactions between homological proteins is not caused by small number of pairs of identical "sticky domains" shared between interacting proteins.
