
	mirPath Help.


	1. The search interface.


	In the next screenshot you can find a demonstration of the most important controls of the mirPath interface: mirPath can accept miRNA lists in the form of a text file. Entries should be miRNA names (miRBase 18 nomenclature) or miRNA MIMAT IDs, each in a new line. Method can be specified after each miRNA identifier using a delimeter '\|'. eg: hsa-let-7a\|Tarbase (default method used microT-CDS) In the next screenshot you can see the format of a sample file:


	2. The results.


	In the next screenshot you can find a demonstration of the pathway results list:


	3. A Priori Methods

Genes Union

This option first calculates the union of targeted genes by the selected microRNAs (UNION_SET: all genes targeted by at least one selected miRNAs). The UNION_SET set is used for the overrepresentation statistical analysis. This enrichment analysis identifies pathways significantly enriched with genes belonging to the UNION_SET. This is an A Priori Analysis Method.

Genes Intersection

In this analysis, the intersection of targeted genes (INTERSECTION_SET: genes targeted by all selected miRNAs) is calculated for the overrepresentation statistical analysis. The enrichment analysis identifies pathways significantly enriched in genes from INTERSECTION_SET. The user has the option to modify inclusion criteria to the INTERSECTION_SET by using the relevant dial on right. With this dial the user can select the minimum number of microRNAs required to target a gene, instead of all selected microRNAs (predefined option). For example, if the user selects 10 microRNAs, the server will calculate the INTERSECTION_SET using the default option. In this set, only the genes targeted by all 10 microRNAs will be included. In cases of large numbers of microRNAs, the INTERSECTION_SET will probably be very small. By using the relevant dial, the user has the option to define the minimum number of required microRNAs (less than 10 in this case). The INTERSECTION_SET is now defined as the set of genes targeted by a number of miRNAs larger or equal to the user defined threshold. For example, by selecting 5 as a threshold, all genes targeted by at least 5 microRNAs will be included to the INTERSECTION_SET (instead of 10). This is an A Priori Analysis Method.


	4. A Posteriori Methods

Pathways Union

In this mode, the server identifies all the significantly targeted pathways by the selected microRNAs. The server initially performs the enrichment analysis and calculates the significance levels (p-values) between each miRNA and every pathway. Subsequently, for each pathway a merged p-value is extracted by combining the previously calculated significance levels, using Fisher’s meta-analysis method. The resulting p-value depicts 1 - the probability that the examined pathway is significantly enriched with gene targets of at least one selected microRNA. In other words, the merged p-values signify if a particular pathway is targeted by at least one miRNA out of the initially selected group. This is an A Posteriori Analysis Method.

Pathways Intersection

This option provides the intersection of targeted pathways by the selected microRNAs. The resulting subset contains only pathways with statistically significant results for all the selected microRNAs. Significance levels are calculated as in the Pathways Union Analysis. In this option only pathways significantly targeted by all selected microRNAs are included. For example, if a pathway is not significantly targeted by one or more microRNAs, then this specific pathway will not be included in the merging step of the analysis. An A Posteriori Analysis Method.