Battery gene sets for CAMERA limma

Battery gene sets for CAMERA limma

1

@e1fb1374

Last seen 8 hours ago

Germany

Hi everyone,

I’m confused with the results of my CAMERA analysis. For building indexes, I used the battery of gene sets from MSigDb. I transformed the gmt files to list and built indexes. The initial count matrixes contained hgnc symbols as row names, which include protein-coding genes, as well as lncRNA, miRNA and etc. names. MSigDb allows users to download two types of sets: entrez ids and hgnc symbols. When I transform symbols to entrez and build indexes the result completely differs from the case when I use symbols for building indexes

Example with symbols to build indexes

camera_res1[1:5,]

                                                  NGenes Direction       PValue          FDR
RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY     98        Up 7.358697e-12 2.267950e-08
KEGG_RIBOSOME                                         85        Up 2.507014e-11 3.863308e-08
EUKARYOTIC_TRANSLATION_ELONGATION                     90        Up 2.086557e-10 1.862321e-07
SELENOAMINO_ACID_METABOLISM                          105        Up 2.417029e-10 1.862321e-07
CELLULAR_RESPONSE_TO_STARVATION                      149        Up 1.376982e-09 8.487719e-07

Example with entrez ids for indexing

camera_res2[1:5,]


                                                      NGenes Direction      PValue       FDR
SIGNALLING_TO_RAS                                         20      Down 0.000617136 0.9982597
PLASMA_LIPOPROTEIN_REMODELING                             19      Down 0.001480280 0.9982597
ACTIVATION_OF_TRKA_RECEPTORS                               2      Down 0.002682050 0.9982597
WP_MEVALONATE_ARM_OF_CHOLESTEROL_BIOSYNTHESIS_PATHWAY     12        Up 0.003880270 0.9982597
NABA_ECM_AFFILIATED                                       85      Down 0.003973647 0.9982597

In the first case(with symbols) I had a larger list of pathways (3082), in the second it was 3041.
What result is more relevant? Do non-protein-coding RNAs play such a crucial role in pathway significance?


CAMERA

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