TFcancer: a manually curated database of transcription factors associated with human cancer 网址：http://lcbb.swjtu.edu.cn/tfcancer/index.html 复制上面的网址，打开以后是这样的 这个数据库很好使用，所有功能一目了然，可以搜索，浏览，下载，上传。浏览的网速也很快。该数据库通过手工整理1800多篇文献，收...
subsampled runs, above which defines significantly enriched motifs. Default=0.01 Optional mapTF arguments: -dist: the distance cutoff (in base pair) for associating TRE to the nearest annotated transcriptional start site. Default=50000. -closest.N: use this tag to report only the first nth ...
TRRUST database also provide information of mode of regulation (activation or repression). Currently 4,861 (60.6%) regulatory relationships are known for mode of regulation. head(TRRUST[["STAT3"]], 100) [1] "A2M" "AKAP12" "AKT1" "BCL2" "BCL2" "BCL2L1" "BCL2L1" "BCL6" "BIRC5"...
TF Target Mapper has support for multiple users, thus data can be compartmentalized into projects/individual investigations. After registering and logging in, the user can view the welcome page with information on the contents of the database (total number of sequences, BLAST hits, BLAST HSPs, ...
Finally, the lower DAPK1 expression in HCC was validated via the GEO database, UALCAN cohort, and qRT-PCR. Conclusion: In conclusion, we established a significant TF-enhancer-target regulatory network and identified downregulated DAPK1 as an important prognostic and diagnostic gene in HCC. Its ...
S1). Further screening using the GEO database revealed 32 proteins that were also elevated in liver cancer (Fig. 1a). To narrow candidates, UniProt (https://www.uniprot.org) and the human protein atlas (THPA, https://www.proteinatlas.org/search) online software, which provides information ...
TFcancer:a manually curated database of transcription factors associated with human cancer 网址:http://lcbb./tfcancer/index.html 复制上面的网址,打开以后是这样的 这个数据库很好使用,所有功能一目了然,可以搜索,浏览,下载,上传。浏览的网速也很快。该数据库通过手工整理1800多篇文献,收录3136个实验支持的364...
Our lists of direction-specific targets for 152 TFs (80.0%) are larger that in the TRRUST database. In average, 30.9% of genes that respond greater than or equal to twofold to the induction of TFs are regulated targets. Regulated target genes indicate that the majority of TFs are either ...
defrun_scenic(adata,tf_names,DATABASES_GLOB,MOTIF_ANNOTATIONS_FNAME):exp_matrix=pd.DataFrame(adata.X.toarray(),columns=adata.var.index,index=adata.obs.index)db_fnames=glob.glob(DATABASES_GLOB)defname(fname):returnos.path.splitext(os.path.basename(fname))[0]dbs=[RankingDatabase(fname=fnam...
subsampled runs, above which defines significantly enriched motifs. Default=0.01 Optional mapTF arguments: -dist: the distance cutoff (in base pair) for associating TRE to the nearest annotated transcriptional start site. Default=50000. -closest.N: use this tag to report only the first nth ...