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Search cis-regulatory sequence combinations |
How to SearchThis means you can search cis-regulatory sequence combinations by using the combination id. e.g.: if you want to search the combination with combination id M101, just simply input M101 as the keyword and then click the Search Combinations! For all 18638 cis-regulatory sequence combiantions, please check s1 in the download directory Download. This means you can search the combinations by using cis-regulatory sequences in combinations. e.g.: if you want to get all the combinations with cis-regulatory sequence 101 and 105. Then you can input the 101,105 as the keywords. Note that you need to use "," to separate multiple cis-regulatory sequence IDs if you have multiple. For all PLACE cis-regulatory sequences, please check s5 in the download directory Download or go to PLACE Database . This means you can search the combinations with specific GO term IDs. e.g.: If you want to search combination whose target genes in Arabidopsis significantly (FDR=0.05) overlap with GO term GO:000896-phosphoglycolate phosphatase activity, then just input GO Term id-"GO:000896" or GO term-"phosphoglycolate phosphatase activity" as the keyword.Please note that only the most significant GO Terms were provided for each combination is this server. If you want to get all combinations, whose target genes significantly (FDR=0.05) overlap with any GO-terms,then input "*" as the keyword. This means you can search the combinations whose target genes significantly (FDR=0.05) overlap with given dataset. e.g.: if you want to search combinations whose target genes significantly overlap with GSE6906, then just input GSE6906 as the keyword. For all GEO datasets information,please check s5 in the download directory Download. If you want to get all the combinations, whose target genes significantly (FDR=0.05) overlap with co-expressed clusters from any of the GEO sets, then input "*" as the keyword. This means you can search the combinations whose target genes significantly overlap (FDR=0.1) with given dataset. e.g.: if you want to search combinations whose target genes significantly overlap with GSE6906, then just input GSE6906 as the keyword. If you want to get all the combinations, whose target genes significantly (FDR=0.1) overlap with co-expressed clusters from any of the GEO sets, then input "*" as the keyword. This means you can search the combinations whose target genes significantly (FDR=0.05) overlap with given bioenergy gene sets. Eleven bioenergy gene sets were used in this server and each one was assigned one functional id number(from 3-13). Detailed information can be found in Table 1 or following description: Cellulose synthesis gene set of Arabidopsis (functional id 3),Cellulose synthesis gene set of Poplar(4),Phenylpropanoid and lignin synthesis gene set of Arabidopsis(5),Phenylpropanoid and lignin synthesis gene set of Poplar(6),Terpenoid synthesis gene set of Arabidopsis(7),Terpenoid synthesis gene set of Poplar(8),Aux/IAA gene set of Arabidopsis(9),Aux/IAA gene set of Poplar(10),Voltage gated ion channel gene set of Arabidopsis(11),TNL gene set of Arabidopsis(12) TNL gene set of Poplar(13).e.g.: If you want to search combinations whose target genes in Arabidopsis significantly overlap(FDR=0.05) overlap with Cellulose synthesis gene set of Arabidopsis(3), then just input "3" as the keywords. Note that multiple key words need to be separated by ",". If you want to get all the combinations,whose target genes overlap with any of these bioenery gene sets, then input "*" as the keyword. This means you can search the combinations which are consistent with known cis-regulatory sequence combinations. Seven known cis-regulatory sequence combinations have been used in this server. They are bzip_bzip,bzip_dof,bzip_myb bhlh_myb,mads_mads,rav1,zmhox2a. e.g.: If you want to search combinations which are consistent with bzip_bzip, just input "bzip_bzip" as the keywords. Mutiple keywords should be sepearted by ",". If you want to get all combinations which are consisent with any of these 7 know combinations, just input "*" as the keyword. This means you can search the combinations with specific target genes in Arabidopsis. e.g.: if you want to search combinations, which have target gene AT1G09665 in Arabidopsis, then input "AT1G09665" as the keyword. Multiple keywords should be seperated by ",". This means you can search the combinations with specific target genes in Poplar. e.g.: if you want to search combinations, which have target gene POPTR_0001s16770 in Poplar, then input "POPTR_0001s16770" as the keyword. Multiple keywords should be separated by ",". |