tftargets使用说明
2019-10-23 本文已影响0人
大吉岭猹
1. 概述
- 这个数据包中含有6个列表，分别是：ENCODE，ITFP，Marbach2016，Neph2012，TRED，TRRUST，他们包含了不同数据来源的转录因子和靶向基因对应关系。
- ENCODE的数据来自(http://hgdownload.cse.ucsc.edu/goldenpath/hg19/encodeDCC/wgEncodeRegTfbsClustered/)
- ITFP的数据来自(http://itfp.biosino.org/itfp)，但该链接已失效，这里放一个这个数据库发表的文章链接(https://academic.oup.com/bioinformatics/article/24/20/2416/259750)
- Marbach2016的数据来自(http://www.regulatorycircuits.org/)
- Neph2012的数据来自(http://www.regulatorynetworks.org/)
- TRED的数据来自(https://cb.utdallas.edu/cgi-bin/TRED/)，可能是网速问题，这个链接我也打不开
- TRRUST的数据来自(http://www.grnpedia.org/trrust/)
2. 数据结构
2.1. ENCODE
> length(ENCODE)
[1] 157
> ENCODE[1]
$ZBTB33
[1] "14" "19" "48" "95" "1025" [6] "2769" "3033" "3054" "3270" "4007" [11] "5467" "5537" "6838" "7172" "7337"
[16] "7375" "7507" "7743" "8541" "10526"
[21] "10753" "10795" "10926" "11322" "23360"
[26] "23518" "25953" "26137" "29128" "51281"
[31] "51422" "51646" "54534" "54623" "54662"
[36] "55051" "55361" "55588" "55656" "55915"
[41] "55972" "56910" "57658" "64175" "79078"
[46] "79649" "79733" "84083" "84303" "84836"
[51] "84957" "93233" "114799" "118812" "126917"
[56] "144501" "148304" "165082" "221458" "221656"
[61] "222256" "283450" "285033" "344595" "348645"
[66] "100131096" "100288069" "100302640" "100526760" "100616250"
- 长度为157的列表，每项包含了一个字符向量，内容是靶向基因的Entrez ID
2.2. ITFP
> length(ITFP)
[1] 1974
> ITFP[1]
$AAAS
[1] "ACSF3" "APRT" "C12orf52" "FBXL19" "G6PC3"
- 长度为1974的列表，每项包含了一个字符向量，内容是靶向基因的symbol
2.3. Marbach2016
> length(Marbach2016)
[1] 643
> Marbach2016[1]
- 长度为643的列表，每项包含了一个字符向量，内容是靶向基因的symbol
2.4. Neph2012
> length(Neph2012)
[1] 41
> Neph2012[["fHeart-DS12531"]][["STAT3"]]
[1] "466" "467" "468" "1050" "1385" "1386" "1390"
[8] "1958" "1959" "1960" "1961" "1999" "2494" "2735"
[15] "2736" "2737" "2969" "4150" "4800" "4801" "4802"
[22] "4807" "5076" "5453" "5454" "6667" "6668" "6670"
[29] "6671" "6774" "7020" "7021" "7022" "7490" "7707"
[36] "8462" "9314" "9586" "10127" "10664" "11016" "22809"
[43] "22926" "29842" "51043" "148979"
- 这个数据相对比较特殊，有两个维度，包含了41种细胞类型中若干种（每种细胞类型不一样）转录因子靶向的其他转录因子（注意不是所有基因）的Entrez ID
2.5. TRED
> length(TRED)
[1] 133
> TRED[1]
$PAX1
[1] "5156" "7428" "9356" "9376" "55210" "118856"
- 长度为133的列表，每项包含了一个字符向量，内容是靶向基因的Entrez ID
2.6. TRRUST
> length(TRRUST)
[1] 748
> TRRUST[1]
$AATF
[1] "BAK1" "BAX" "BBC3" "CDKN1A" "MYC" "TP53"
- 长度748的列表，每项包含了一个字符向量，内容是靶向基因的Entrez ID
