然后,再利用咱们北大的plantTFDB这个软件下载不同物种matrix(*.meme) http://planttfdb.cbi.pku.edu.cn/download.php#bind_motif 最后使用MEME套件的 fimo 工具来进行预测。 fimo --oc . --verbosity 1 --thresh 1.0E-5 Ath_TF_binding_motifs.meme promoter.fa 这样我们基因组上的转录因子和转录因子结合位点...
Binding Motifs 获取 打开Plant TF Binding Motif Shift 插件,设置苹果的蛋白序列全集,设置输出文件路径前缀,点击 Start 即可 等待即可(由于是几万个蛋白序列比对到几万个蛋白序列,如果是一般笔记本,BLAST的话,可能需要跑一整个晚上,但这个是值得的,因为一个物种一般就跑一次就好了。BLAST到底还是会比DIAMOND这类准确一...
Hepatocyte nuclear factor 3 (winged helix domain) activates trefoil factor gene TFF1 through a binding motif adjacent to the TATAA box. DNA Cell Biol 1999; 18 :157–64. [ PubMed ]Beck S,Sommer,Blin N,et al.Hepatocyte nuclear factor 3 (winged helix domain) activates trefoil factor gene ...
Phylogenetic footprinting analysisMotif profileTranscription factorsBinding sitesTranscription regulationLysR-type transcription regulator familyLTTRThe goal of most programs developed to find transcription factor binding sites (TFBSs) is the identification of discrete sequence motifs that are significantly over-...
d, ChIP-qPCR analysis for the putative E2F4 binding sites of indicated gene loci. eHAP cells were cultured with or without 5 µM HLM006474. (the left panel). Growth curves of eHAP cells treated with the indicated concentration of HLM006474 (the right panel). Statistics: a two-tailed ...
E qRT‒PCR analysis of the four anticipated targets in A549-vector and A549-TFAP2A cells revealed a significant alteration ESR2 expression. F The relative levels of TFAP2A and ESR2 after TFAP2A overexpression or knockdown. G The binding motif of TFAP2A was identified, and two potential ...
Moreover, they do not fully exploit the ChIP-seq peak information such as the enrichment for the TF canonical binding motif close to the ChIP-seq peak summit - where most of the reads align [18]. To address these limitations, we recently developed the ChIP-eat software to specifically ...
binding. Thus, its core sequence was identified as “TGTCGC,” and it was named the TC-box. Similarly, the third DNA base (C) on the right boundary of motif 3 was essential for BplMYB46 binding. The core sequence of motif 3 was identified as “AGTAGTTC,” and it was named the ...
2. FOXA2 binding sites features in HNF4A ``` cd code_for_analysis/FOXA2_in_HNF4A #from the root directory python analyse_FOXA2_feature.py ``` Expected final output: Reference run time for this step: 0:15.94, 125% CPU-Util 3. Generate obvious TFBS feature ``` cd code_for_anal...
RREB-1 and SP-1 are members of the zinc finger protein family with different binding specificities. However, the consensus of both matrices in JASPAR are very similar, being constituted of several occurrences of the motif CCCC [14]. 3. A SQUA site that overlaps the third SRF active site...