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Hox AND "systems Biology"

Meeta P Pradhan, Akshay Desai, Mathew J Palakal
BACKGROUND: Epigenetics refers to the reversible functional modifications of the genome that do not correlate to changes in the DNA sequence. The aim of this study is to understand DNA methylation patterns across different stages of lung adenocarcinoma (LUAD). RESULTS: Our study identified 72, 93 and 170 significant DNA methylated genes in Stages I, II and III respectively. A set of common 34 significant DNA methylated genes located in the promoter section of the true CpG islands were found across stages, and these were: HOX genes, FOXG1, GRIK3, HAND2, PRKCB, etc...
2013: BMC Systems Biology
Michael W Hughes, Ping Wu, Ting-Xin Jiang, Sung-Jan Lin, Chen-Yuan Dong, Ang Li, Fon-Jou Hsieh, Randall B Widelitz, Cheng Ming Chuong
The mythological story of the Golden Fleece symbolizes the magical regenerative power of skin appendages. Similar to the adventurous pursuit of the Golden Fleece by the multi-talented Argonauts, today we also need an integrated multi-disciplined approach to understand the cellular and molecular processes during development, regeneration and evolution of skin appendages. To this end, we have explored several aspects of skin appendage biology that contribute to the Turing activator/inhibitor model in feather pattern formation, the topo-biological arrangement of stem cells in organ shape determination, the macro-environmental regulation of stem cells in regenerative hair waves, and potential novel molecular pathways in the morphological evolution of feathers...
April 2011: Integrative Biology: Quantitative Biosciences From Nano to Macro
Ming-Jiun Yu, R Lance Miller, Panapat Uawithya, Markus M Rinschen, Sookkasem Khositseth, Drew W W Braucht, Chung-Lin Chou, Trairak Pisitkun, Raoul D Nelson, Mark A Knepper
We used a systems biology-based approach to investigate the basis of cell-specific expression of the water channel aquaporin-2 (AQP2) in the renal collecting duct. Computational analysis of the 5'-flanking region of the AQP2 gene (Genomatix) revealed 2 conserved clusters of putative transcriptional regulator (TR) binding elements (BEs) centered at -513 bp (corresponding to the SF1, NFAT, and FKHD TR families) and -224 bp (corresponding to the AP2, SRF, CREB, GATA, and HOX TR families). Three other conserved motifs corresponded to the ETS, EBOX, and RXR TR families...
February 17, 2009: Proceedings of the National Academy of Sciences of the United States of America
John L Rinn, Jordon K Wang, Helen Liu, Kelli Montgomery, Matt van de Rijn, Howard Y Chang
Human skin exhibits exquisite site-specific morphologies and functions. How are these site-specific differences specified during development, maintained in adult homeostasis, and potentially perturbed by disease processes? Here, we review progress in understanding the anatomic patterning of fibroblasts, a major constituent cell type of the dermis and key participant in epithelial-mesenchymal interactions. The gene expression programs of human fibroblasts largely reflect the superimposition of three gene expression profiles that demarcate the fibroblast's position relative to three developmental axes...
April 2008: Journal of Investigative Dermatology
A H Bass, R Baker
This essay considers the ontogeny and phylogeny of the cranial neural circuitry producing rhythmic behaviors in vertebrates. These behaviors are characterized by predictable temporal patterns established by a neuronal network variously referred to as either a pacemaker, neural oscillator or central pattern generator. Comparative vertebrate studies have demonstrated that the embryonic hindbrain is divided into segmented compartments called rhombomeres, each of which gives rise to a distinct complement of cranial motoneurons and, as yet, unidentified populations of interneurons...
1997: Brain, Behavior and Evolution
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