Select any of the sections to view the results of the corresponding data. There are two main modes of querying regardless of the data source you select: \nmotif based query (or source query) and gene/target-id based query (target query).
\nOne result of a source having a score in one of the target regions is called a hit.
\nThe data source determines what kind of hits you will be querying and which species or region of genome those hits come from.
\nIn this mode, you can select a source, be it a motif for MotifMap based results or a TF for ChIPSeq, and then find its targets across the genome.
\nYou can select a variety of filtering parameters to narrow down your search. The details on the parameters are explained below in their corresponding section.
\nIn most cases, you will be able to select a row from a table of motifs/TFs and conduct your search based on that motif. This table, along with all the other tables from this site, is fully interactive.\nYou can sort, search by keyword and download results into xls format.
\nOnce you determine the motif and the parameter. Press the button to show target results. In some cases, if you select any row from the output, you can utilize a link below the table to view extra annotations for that row.\nDoing so will open a new window.
\nIn this mode, you can select a target, be it a gene or a miRNA or a UTR region, and then query the database for all sources (motifs etc) that have hits within the target region.
\nYou can again use a variety of filtering parameters to narrow down your search.
\nThe results are presented in a similar way as motif based queries and you can sometimes view additional annotations in the same way.
\nTogether these two methods provides you a powerful toolset for discovering potential binding relationships between regulating factors and their target regions.
\nMotif Selection in Motif Search
\nIn the Motif Search mode, there is an interactive table containing all the motifs from MotifMap-RNA. You can select a row, see additional\nannotations from CISBP or RBPDB by clicking the corresponding buttons, or start a search using the specified filtering parameters. This table\ncontains the following columns: ID, this is the ID used by MotifMap-RNA, CISBP-ID this is the ID of the corresponding CISBP motif, if such exists,\nRBPDB-ID this is the ID of the RBPDB motif, if such exists. Note that ID matches either of these two and whichever it matches is the source of \nthis motif. Name and Original Species contain basic annotations for the selected motif.
\nAdditionally, when you click on a motif (row), you will see a motif LOGO if it exists. Some motifs may be very short and degenerate, \nand as a result the hits are not as reliable as those from a longer, more specific motif. In these cases you may want to increase the filtering\nthresholds, and especially take advantage of genomic distance filtering to localize potential hits. Aggregate z-scores and BBLS may also \nindicate more reliable hits.
\nIf you have questions on the quality or origin of the motif, you can check the annotations from CISBP or RBPDB, which typically include the publication\nthat the motif is derived from.
\nFiltering parameters:
\nz-score is the main indicator of the strength of predicted binding. It is specific to the binding motif (in PWM form) and the target sequence of the exact site.
\nWeighted z-score is a form of meta z-scores that has exponentially decaying weight based on the local ranking of z-scores of the hits. It compensates the main z-score by considering the potential\nlocal clustering of binding sites. It will always be higher than z-score. \nOne effective method of filtering strategy is to filter based on a relatively low z-score but a high Weighted z-score.
\nBBLS is Bayesian Branch Length Score, which is a measure of how conserved the binding site is across the phylogentic tree near the targetted species. It is proven to be an effective indicator of \nconservativity of hits. However, in the case of RBP hits, sometimes it is absent for strong hits and may not be the best primary filtering parameters. However, you can sort the results by it in the results table.
\nUpstream and Downstream indicates the distances in bp from the transcription start site (TSS) of the target gene or the closest gene. In some cases this is highly effective as a filtering parameter while in others\nit will be meaningless. Note: in the case of intronic data, this parameter filters for the distance relative to the intron start site.
\nWhen counting distances, the strandity of the hit and the target gene are always considered. However, in presenting the genomic location in the form of genome coordinates, we never use negative connotations. All positions\nare based on the positive strand.
\nResults intepretation:
\nSeqID is the assigned sequence ID for the hit. Usually this is generated by MotifMap-RNA but for LNC we keep the NONCODE ID.
\nChr, Start and Stop show the genome coordinate of the hit, always on the positive strand.\nStrand indicates the actual strandity of the hit. We provide both the strand of the hit (as Strand) and the strand of the closest genomic annotation (ClosestGeneStrand),\nin many cases if the two differ the hit is not very relevant. Since the strand of the reference is always the same, you can sort by hit strand to easily see all hits on that same strand.
\nZScore is the main factor indicating the strength of potential binding. Please note that in the case of short motifs there can exist many hits with max ZScores.
\nWeightedZ is an aggregate ZScore exponentially weighted by ranks. It is similar to StoufferZ which is linearly weighted by rank.\nThese two scores indicate local clustering of strong hits and are more scalable than ZScores. If you find many hits with the same max ZScores they will help you identify those with more strong hits in its vicinity.
\nBBLS indicates conservativity of the hit, a score of 1 is significant while 4 is very strongly conserved. Edges indicates in how many phylogenetic neightbor does the hit likely exist.
\nClosestGene indicates the closest gene to the hit, regardless of the type of \nhit. The distances to CDS and TSS are presented as well.
\nIn the case of a gene search, the gene information is replaced by motif information. Additional links to CISBP or RBPDB is are also provided when you click on a row.
\nMotifMap documentation is currently available at MotifMap website
\nWe house ChIP-Seq data derived from ENCODE or GEO public data. More information pending.
\n