接着,选择TF-gene Interaction database,我们这里选择JASPAR数据库用于转录因子的预测。 很快,TF-gene的互作网络就完成了构建,如下,点击SIF,可下载sif格式的网络图文件导入到Cytoscape中进行分析和展示。 继续点击Proceed按钮,我们可以预览构建的TF-gene互作网络,默认的效果如下。 当然,我们也可以将网络图的背景调成白色...
点击上传、下一步,选择TF-gene interaction: image.png 这里选择steiner forest network: image.png 再点击下一步,最后下载sif文件: image.png 将subnetwork1.sif导入cytoscape(network from file),将subnetwork1_Types.NA重新整理成一个两列的文件,第一列为基因名,第二列为属性(基因or转录因子): image.png 然后...
Infer the cell-cell communication score The communication score of an L-R interaction between cell types is evaluated by integrating the L2- norm of the L-R interaction and the activity score of the downstream TFs. mt <- TransCommuProfile(object = mt, pValueCor = 0.05, CorValue = 0.1, ...
(3) among the SDO (synthetic with Dst one), SOH1 shows the strongest genetic interaction with DST1; (4) the presence of multiple copies of TAF14, SUA7, GAL11, RTS1, and TYS1 alleviate the growth phenotype of dst1 soh1 mutants; and (5) SRB5 and SIN4 genetically interact with DST...
接下来按节点之间的互作关系分别研究 选择其中的一种互作关系 Interaction里边包含了互作的miRNA-gene对;ORA分析显示了显著富集GO term,KEGG等term的结果;最后是通过网络挖掘出的motif分析。 想学习更多,请关注云生信学生物信息学微信公众号。 生信小罗罗 最近更新:03-2808:15 简介:认真讲科研,认真讲故事 作者最新文章...
involved in these motifs: miRNA–gene (miRNA represses gene expression); miRNA–TF (miRNA represses TF gene expression); TF–miRNA (TF regulates miRNA expression); TF–gene (TF regulates gene expression); gene–gene (gene and gene interaction); and miRNA–miRNA (miRNA and miRNA interaction)....
- Function 2: interaction with gene-specific transcription factor 功能2:与基因特异性转录因子相互作用 TFIID can participate in stimulation by Sp1, but TBP cannot → TAFs as coactivators TFIID可以参与Sp1介导的转录激活,但TBP不能,说明TAF作为辅激活因子 ...
Paragraph 3:Another constraint on natural selection is developmental interaction. The different components of an individual organism—its structures and organs—are not independent of one another, and none of them responds to selection without interacting with the others. The whole developmental machinery...
Qpath: a method for querying pathways in a protein-protein interaction network. BMC Bioinformatics. 2006; 7:199. doi:10.1186/1471-2105-7-199. Article PubMed PubMed Central Google Scholar Bebek G, Yang J. Pathfinder: mining signal transduction pathway segments from protein-protein interaction ...
Sterol regulation of 3-hydroxy-3-methylglutaryl-coenzyme A synthase gene through a direct interaction between sterol regulatory element binding protein and the trimeric CCAAT-binding factor/nuclear factor Y. J Biol Chem. 1998;273(3):1349–56. Article CAS PubMed Google Scholar Lee LC, Chen CM,...