Hello, The format of the identifiers is part of the reason why some are not returned. For example:
your list: V$AP-1_01 browser table: V$AP1_01 your list: V$c-myb_01 browser table: V$CMYB_01 Perhaps download the names first as a file to determine the correct format (and which are in the dataset or not, regardless of formatting) and then try one of the following: Best option: 1) Download the tables and use your own tools to perform a search using a shell/perl script that can add in some flexibility to the naming with regular expressions (in particular, this would get around the version match problem). Some reformatting may still be necessary. Table are on the downloads server, organized by assembly, in the Database tables (goldenPath/<db>/database/<mysql_files_here>). Ftp instructions: http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 Other possible options 2) Correct the names and upload the list into the Table browser. You could include all versions in the same list. The identifier function does not allow for regular expression use - the names must be exact to be extracted. 3) Use the public mySQL database to write a SQL query that allows more flexibility in the name by using a combination of wildcards and some reformatting of the names. http://genome.ucsc.edu/FAQ/FAQdownloads.html#download29 4) Use the Table browser and the "filter" function to write the names as a free-form mySQL query, that again has some reformatting of the name plus wildcard characters. This would be tedious since each would have to be done independently. Hopefully one of these will work for you, Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/23/10 3:24 AM, Tapas wrote: > At UCSC Genome Browser: > > > > clade: Mammal, > > genome: Human, > > assembly: Mar. 2006, > > group: Regulation, > > track: TFBS Conserved, > > table: tfbsConsSites and tfbsConsFactors. > > > > Finally paste list like > > > > V$AML1_01 > > V$AP-1_01 > > V$BCR_01 > > V$BMP2_01 > > V$BMP6_01 > > V$BRCA1_01 > > V$C/EBPa_01 > > V$CCND1_01 > > V$c-myb_01 > > V$CREB_01 > > V$E2F_01 > > V$E6_01 > > V$EGR1_01 > > V$EIF2C2_01 > > V$Eralpha_01 > > V$FOXP3_01 > > V$FSH_01 > > V$GATA1_01 > > V$HIF1A_01 > > V$HMGA1_01 > > V$HNF1A_01 > > V$HoxD10_01 > > V$IL1B_01 > > V$LMO2_01 > > V$LPS_01 > > V$MECP2_01 > > V$MEF2_01 > > V$MRF4_01 > > V$MRF5_01 > > V$MYC_01 > > V$MYCN_01 > > V$MYF5_01 > > V$MyoD_01 > > V$Myogenin_01 > > V$NFIB_01 > > V$NFKB1_01 > > V$NKX2-5_01 > > V$NR3B3_01 > > V$PDGF_01 > > V$PLZF_01 > > V$PRKCA_01 > > V$PTEN_01 > > V$REST_01 > > V$Rex1_01 > > V$RUNX1_01 > > V$SHP_01 > > V$SIP1_01 > > V$SMAD4_01 > > V$SOX2_01 > > V$SP1_01 > > V$TGFB1_01 > > V$Thrombin_01 > > V$TLR2_01 > > V$TLR4_01 > > V$TLR7_01 > > V$TLR8_01 > > V$TLX_01 > > V$TLX1_01 > > V$TLX3_01 > > V$TNF-alpha_01 > > V$TP53_01 > > V$TRIM32_01 > > V$TWIST1_01 > > V$VHL_01 > > V$YY1_01 > > V$ZEB1_01 > > V$ZEB2_01 > > > > > > But i get information only about 9 TFs using version 01. Similarly using > version 02 I get 5 TFs, version 03-> 3 TFs, version 04-> 2 TFs, version 05-> > 1 TFs, version 06-> 1TFs. Total I get 21 TFs . Among which # unique TFs= 9. > How can i get info about rest 58 TFs. Pls. help me. > > This mail is scanned by Ironport > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
