Abstract:In this paper, we present a method for core-attachment complexes identification based on maximal frequent patterns (CCiMFP) in yeast protein-protein interaction (PPI) networks. Firstly, we detect subgraphs with high degrees as candidate protein cores by mining maximal frequent patterns. Then using topological and functional similarities, we combine highly similar protein cores and filter insignificant ones. Finally, the core-attachment complexes are formed by adding attachment proteins to each significant core. We experimentally evaluate the performance of our method CCiMFP on yeast PPI networks. Using gold standard sets of protein complexes, Gene Ontology (GO), and localization annotations, we show our method gains an improvement over previous algorithms in terms of precision, recall, and biological significance of the predicted complexes. The colocalization scores of our predicted complex sets are higher than those of two known complex sets. Moreover, our method can detect GO-enriched complexes with disconnected cores compared with other methods based on subgraph connectivity.

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	1. Identification of core-attachment complexes based on maximal frequent patterns in protein-protein interaction networks
	YU Liang,GAO Lin,KONG Chuiliang
	Biology 06 April 2011
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	Abstract:In this paper, we present a method for core-attachment complexes identification based on maximal frequent patterns (CCiMFP) in yeast protein-protein interaction (PPI) networks. Firstly, we detect subgraphs with high degrees as candidate protein cores by mining maximal frequent patterns. Then using topological and functional similarities, we combine highly similar protein cores and filter insignificant ones. Finally, the core-attachment complexes are formed by adding attachment proteins to each significant core. We experimentally evaluate the performance of our method CCiMFP on yeast PPI networks. Using gold standard sets of protein complexes, Gene Ontology (GO), and localization annotations, we show our method gains an improvement over previous algorithms in terms of precision, recall, and biological significance of the predicted complexes. The colocalization scores of our predicted complex sets are higher than those of two known complex sets. Moreover, our method can detect GO-enriched complexes with disconnected cores compared with other methods based on subgraph connectivity.
	TO cite this article:YU Liang,GAO Lin,KONG Chuiliang. Identification of core-attachment complexes based on maximal frequent patterns in protein-protein interaction networks[OL].[ 6 April 2011] http://en.paper.edu.cn/en_releasepaper/content/4420342


	2. The complete mitochondrial genome and gene features of Orinoco Crocodile (Crocodylus intermedius)
	Wang Yishu,Zhang Man,Yan Peng,Wu Xiaobing
	Biology 07 March 2011
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	Abstract:The complete mitochondrial genome (mtDNA) of the Orinoco Crocodile (Crocodylus intermedius) was sequenced in our study in order to examine its genome structure. The size of the molecule is 16,828 nucleotides, encodes 22 tRNAs, 13 protein-coding genes, 2 rRNAs, and a control region (D-loop). The organization of the new mt genome is consistent with other crocodilians that have been published so far. They all show the rearrangement of two tRNA genes (tRNAPhe and tRNASer(AGY)) which is different from typical vertebrates structure. It reveals that the gene order of crocodilians is remarkably conserved.
	TO cite this article:Wang Yishu,Zhang Man,Yan Peng, et al. The complete mitochondrial genome and gene features of Orinoco Crocodile (Crocodylus intermedius)[OL].[ 7 March 2011] http://en.paper.edu.cn/en_releasepaper/content/4414949

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	3. Application of peptide retention time in proteome research
	SHAO Chen,GAO Youhe
	Biology 22 February 2011
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	Abstract:Liquid chromatography coupled with mass spectrometry (LC-MS) has been one of the most popular approaches in proteome analysis. As an independent parameter to mass spectrometry information, peptide retention time has been utilized to facilitate protein identification and quantification. In the filed of peptide identification, prediction of the retention time combined with routine tandem mass spectrometry (MS/MS) database searching methods could help improve the confidence of identification. The sensitivity of identification could also be improved by matching peaks with both the accurate mass and retention time in multiple aligned LC-MS runs. Meanwhile, because small changes of liquid chromatography(LC) conditions lead to variability in retention times unavoidably，retention time alignment is crucial to label-free quantification. Additionally，post-translational modifications (PTM) could be identified by combining retention time shifts and mass deviation information.
	TO cite this article:SHAO Chen,GAO Youhe. Application of peptide retention time in proteome research[OL].[22 February 2011] http://en.paper.edu.cn/en_releasepaper/content/4411659


	4. HuD regulates the cpg15 expression via its 3'-UTR
	WANG Zhonghui,LI Shujing,Qi Yao,LIU Xiaoyan,ZHAO Jingjing,HAN Yu,CHEN Xianhua,XU Ping
	Biology 11 January 2011
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	Abstract:The candidate plasticity related gene 15 (cpg15) plays important roles in neural development and plasticity. In the present study, we studied the role of the cpg15 3'-untranslated region (UTR) in regulating the expression of the gene. The results showed that the presence of the 3'-UTR significantly decreases, while the absence of the 3'-UTR increases the cpg15 expression, indicating that the 3'-UTR may be critical for regulation of cpg15 expression. In addition, HuD, a neural-specific RNA binding protein, increased the cpg15 expression, which depends on the presence of the 3'-UTR. The results suggest that HuD regulates the cpg15 expression via the 3'-UTR-mediated mechanism.
	TO cite this article:WANG Zhonghui,LI Shujing,Qi Yao, et al. HuD regulates the cpg15 expression via its 3'-UTR[OL].[11 January 2011] http://en.paper.edu.cn/en_releasepaper/content/4405989


	5. Detection of microRNA with low abundance in serum of schizophrenia patients
	Shi Wenting ,Du Jinglun ,Qi Yuhua ,Liang Gaofeng ,Wang Tianyu ,Li Shuchun ,Yang Ke,Xie Shiping ,Xiao Zhongdang
	Biology 25 November 2010
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	Abstract:Recent studies have revealed that aberrant expression of serum miRNA can directly reflect disease status. However, the study of serum miRNA for schizophrenia has not been reported so far. In this paper, the expression levels of serum miR-346 which is the most promising miRNAs to reflect schizophrenia status are studied. Semi-nested qRT-PCR was developed to detect miR-346 with very low abundance in serum sensitively and specifically. The results showed that the expression levels of miR-346 were significantly higher in schizophrenia patients than those in normal subjects. Compared with family schizophrenia patients, circulating miR-346 was significantly higher in sporadic schizophrenia, indicating that there is a positive correlation of circulating miRNA-346 level between schizophrenia patients with and without family history.
	TO cite this article:Shi Wenting ,Du Jinglun ,Qi Yuhua , et al. Detection of microRNA with low abundance in serum of schizophrenia patients[OL].[25 November 2010] http://en.paper.edu.cn/en_releasepaper/content/4393256


	6. Both genome RNA3 and satellite RNA have a role in the biological properties of cucumber mosaic virus Pseudorecombinant
	Jin Leilei,Qin Zuodong,Xu Fangjiao,Zhang Jingwei,Yan Shijie,Chen Jishuang
	Biology 11 October 2010
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	Abstract:Three Cucumber mosaic virus (CMV) Pseudorecombinants were constructed by infectious genomic clones of CMV-Fny and CMV- Tsh in vitro. Each pseudorecombinant displayed different symptoms on the same host plants. Biological phenotype analysis showed the genome RNA3 of CMV-Tsh was an important virulence determinant of pseudorecombinant viruses when inoculated on N. glutinosa and N. benthamiana. Co-infected with satRNA-Tsh, the induced symptoms were all attenuated on N. glutinosa and N. benthamiana. The Northern Blot results showed that satRNA-Tsh apparently attenuated the symptoms by depressing the accumulation of genomic RNAs.
	TO cite this article:Jin Leilei,Qin Zuodong,Xu Fangjiao, et al. Both genome RNA3 and satellite RNA have a role in the biological properties of cucumber mosaic virus Pseudorecombinant[OL].[11 October 2010] http://en.paper.edu.cn/en_releasepaper/content/4387850


	7. The complete genome and gene structure of mitochondrial DNA of African slender-snouted crocodile (Crocodylus cataphractus)
	Zhang Man ,Li Yan,Wang Yishu ,Wu Xiaobing
	Biology 17 March 2010
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	Abstract:The complete mitochondrial genome (mtDNA) of the African slender-snouted crocodile (Crocodylus cataphractus) was sequenced in this article. The whole length of the genome is 16,847 base pairs (bp). Just like other vertebrates, it has codes for 22 tRNAs, 13 protein-coding genes, 2 rRNAs, as well as a control region (D-loop). The gene order and the rearrangement of tRNA genes (tRNAPhe and tRNASer(AGY)) conform to that of other crocodilians sequenced, differing from typical vertebrates structure. It shows again that the gene order of crocodilians is considerably conserved.
	TO cite this article:Zhang Man ,Li Yan,Wang Yishu , et al. The complete genome and gene structure of mitochondrial DNA of African slender-snouted crocodile (Crocodylus cataphractus)[OL].[17 March 2010] http://en.paper.edu.cn/en_releasepaper/content/40799


	8. Soluble expression and two-step purification of the cytoplasmic domains of Arabidopsis CORYNE in Escherichia coli
	Qu Wei,Zhao heng,Li ShuZhen,Luo Yunbo
	Biology 02 March 2010
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	Abstract:CORYNE (CRN) is a receptor-like protein kinase involved in control of Arabidopsis stem cell proliferation with CLAVATA2. To produce large amounts of soluble cytoplasmic kinase domains of CRN from Escherichia coli, three vectors were constructed using a double tag strategy, named pGEX-CRN, pMAL-CRN and p30-CRN. An auto-induction protocol was used to enhance the overproduction of soluble recombinant CRN with a 32Y media at 28 °C. The production of soluble recombined CRN of these vectors was analyzed and the pGEX-CRN was chosen for large-scale protein production. The dual-tagged GST-CRN-His6 was purified in a two-step affinity chromatography and analyzed for autokinase activity.
	TO cite this article:Qu Wei,Zhao heng,Li ShuZhen, et al. Soluble expression and two-step purification of the cytoplasmic domains of Arabidopsis CORYNE in Escherichia coli[OL].[ 2 March 2010] http://en.paper.edu.cn/en_releasepaper/content/40350


	9. Different Cucumber mosaic virus-mediated Regulations of Diseases caused by Tomato mosaic virus in two Tomato Varieties
	Li Yixing ,Guo Hong,Chen Shaoning,Chen Jishuang
	Biology 02 March 2010
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	Abstract:Cucumber mosaic virus (CMV) and Tomato mosaic virus (ToMV) are two principal viruses infecting tomato (Lycopersicon esculentum Mill). In this work, CMV-mediated regulations of diseases caused by ToMV in two tomato varieties were different. When tomato cv. Hezuo 903 plants were first inoculated with CMV-Fny, and then followed by a second inoculation with ToMV-N5 after 6-8 days, plants with co-infection expressed CMV-Fny-induced symptoms. The ToMV-N5-induced necrosis just localized on the inoculated leaves. Typical interference could be summarized for this phenomenon. Systemic necrosis induced by ToMV-N5 and interference between CMV-Fny and ToMV-N5 could not occur in another variety tomato cv.Zhongshu 4. They performed mild mosaic and synergism instead. Different ToMV-N5-induced symptoms in two varieties may be the primary reason of dissimilar ToMV-N5 infections mediated by CMV-Fny. Genotypes of resistance gene Tm2 in tomato cv. Hezuo 903 and Zhongshu 4 had been identified. Results revealed that two tomato varieties genotypes were both consistent with symptoms induced by ToMV-N5. Based on above results, we speculate that different genotypes of Tm2 may bring the difference of ToMV-N5-induced symptoms in two varieties, and this difference may lead dissimilar ToMV-N5 infections mediated by CMV-Fny.
	TO cite this article:Li Yixing ,Guo Hong,Chen Shaoning, et al. Different Cucumber mosaic virus-mediated Regulations of Diseases caused by Tomato mosaic virus in two Tomato Varieties[OL].[ 2 March 2010] http://en.paper.edu.cn/en_releasepaper/content/40344


	10. Vertical and Horizontal cDNA Subtractions Reveal Tissue- Specific Unigenes for Potato Tuberization
	Yao Xinling,Hong Zhiping,Wu Qing,Fan Huihua
	Biology 26 February 2010
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	Abstract:Potato tuberization is a unique biologic process in Solanaceous plants. However, a few are known yet on which genes are involving in metabolism of the process. To dig genes related to tuberization in full transcriptome wide, with leafs and stems/stolons of the early- and late-mature genotypes, 4 vertical and 7 horizontal cDNA subtraction hybridizations were done and led to 11 cDNA libraries constructed. Libraries screening, ESTs sequencing, Reverse Northern Blotting and database search revealed that 217 unigenes from nucleus, choroplasm and mitochondrial genome expressed in leafs and stems/stolons related to tuberization. Data analysis indicated that 1) glucose metabolism companying by a strong redox activation in leafs, a week redox and catalysis level in stems leads to a late formation of stolon. 2) A strong redox activation resulting from lipid and protein metabolisms in stems and a low level of catalysis in leaf is necessary for a early stolon formation.3) it is dehydrin, an unique recognized metabolite, occurring in stems after, rather than before tuberzation. As a conclusion, changes of redox reactions and metabolism lead to either no or early/late tuberization. All above is identical with experiment conclusions reported and deepen our understanding of stolon and tuber formation.
	TO cite this article:Yao Xinling,Hong Zhiping,Wu Qing, et al. Vertical and Horizontal cDNA Subtractions Reveal Tissue- Specific Unigenes for Potato Tuberization[OL].[26 February 2010] http://en.paper.edu.cn/en_releasepaper/content/40261

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