The mosdef User’s Guide (original) (raw)
mosdef allows you to create your enrichment results right from your DESeqDataset and DESeqResults objects using 3 possible algorithms, widely used:
For more information on the differences between these algorithms we refer to their individual vignettes and publications.
All of these algorithms require an annotation to function properly, so make sure you have installed and use the correct one for your experimental data. The default is org.Mm.eg.db (Mus musculus). The macrophage data however stems from human, so we need org.Hs.eg.db, and we load this package in the following chunk:
We also want to add a symbol column for later use - and, in order to add a human readable name for our features of interest:
We indeed recommend to use identifiers as row names that are machine-readable and stable over time, such as ENSEMBL or GENCODE.
To ensure that we are using objects that would work out-of-the-box into mosdef, we provide some utilities to check that in advance - this can relax the need of specifying a number of parameters in the other functions.
mosdef and topGO
topGO is a widely used option to obtain a set of spot-on Gene Ontology terms, removing some of the more generic ones and therefore also reducing the redundancy which is inherent in the GO database (Ashburner et al. 2000).
library("topGO")
#> Loading required package: graph
#> Loading required package: GO.db
#> Loading required package: SparseM
#>
#> groupGOTerms: GOBPTerm, GOMFTerm, GOCCTerm environments built.
#>
#> Attaching package: 'topGO'
#> The following object is masked from 'package:IRanges':
#>
#> members
res_enrich_macrophage_topGO <- run_topGO(
de_container = dds_macrophage,
res_de = res_macrophage_IFNg_vs_naive,
ontology = "BP",
mapping = "org.Hs.eg.db",
FDR_threshold = 0.05,
gene_id = "symbol",
de_type = "up_and_down",
add_gene_to_terms = TRUE,
topGO_method2 = "elim",
min_counts = 20,
top_de = 700,
verbose = TRUE
)
#> 'select()' returned 1:many mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
#> Your dataset has 1024 DE genes.
#> You selected 700 (68.36%) genes for the enrichment analysis.
#> You are analyzing up_and_down-regulated genes in the `res_de` container
#> Warning in run_topGO(de_container = dds_macrophage, res_de =
#> res_macrophage_IFNg_vs_naive, : NAs introduced by coercion
#> 6071 GO terms were analyzed. Not all of them are significantly enriched.
#> We suggest further subsetting the output list by for example:
#> using a pvalue cutoff in the column:
#> 'p.value_elim'.The run_topGO function will return a table with the analysis for all possible GO terms (currently when using the “BP” ontology on the macrophage dataset that is 6071 terms). Not all of these results are significant, and this list can (should) be further subset/filtered. For example by using a p-value cutoff.
The key parameters for run_topGO() are defined as follows:
de_container: YourDESeqDatasetobjectres_de: YourDESeqResultsobjectontology: Which gene ontology to analyse, default is “BP”mapping: The annotation/speciesgene_id: Which format the genes are provided. If you provide aDESeqDatasetandDESeqResults, then mosdef does it for you and uses symbols. If you provide vectors please specify a value.FDR_threshold: The pvalue to use to count a gene as significant. The default is 0.05 but if you want a stricter analysis you could set this to 0.01 for examplede_type: Which genes to analyse. The default is all (“up_and_down”) Other possibilities are only up-/down-regulated (“up”/“down”) genes.add_gene_to_terms: Logical, whether to add a column with all genes annotated to each GO term.topGO_method2: Character, specifying which of the methods implemented bytopGOis to be used. The default is elim. For more info look at the documentation of topGO.min_counts: Minimum number of counts a gene has to have to be considered for the background. The default is 0 and we advise this parameter is only used by expert users that understand the impact of selecting “non-standard” backgrounds.top_de: The number of genes to be considered in the enrich analysis. The default is all genes, this can be reduced to reduce redundancy. In this case, we take the top 700 highest DE genes based of padj score. If this number is bigger than the total amount of de genes the parameter defaults back to all genes.verbose: Whether or not to summarise the analysis in a message.
head(res_enrich_macrophage_topGO)
#> GO.ID
#> 1 GO:0002250
#> 2 GO:0002503
#> 3 GO:0019886
#> 4 GO:0045087
#> 5 GO:0034341
#> 6 GO:0001916
#> Term
#> 1 adaptive immune response
#> 2 peptide antigen assembly with MHC class II protein complex
#> 3 antigen processing and presentation of exogenous peptide antigen via MHC class II
#> 4 innate immune response
#> 5 response to type II interferon
#> 6 positive regulation of T cell mediated cytotoxicity
#> Annotated Significant Expected Rank in p.value_classic p.value_elim
#> 1 384 89 15.97 3 4.0e-21
#> 2 13 13 0.54 26 9.5e-19
#> 3 27 15 1.12 53 1.7e-14
#> 4 784 104 32.61 16 1.6e-11
#> 5 110 28 4.58 49 5.2e-11
#> 6 31 13 1.29 102 9.8e-11
#> p.value_classic
#> 1 NA
#> 2 9.7e-19
#> 3 1.7e-14
#> 4 3.2e-27
#> 5 4.9e-15
#> 6 1.0e-10
#> genes
#> 1 ASCL2,B2M,BTN3A1,BTN3A2,BTN3A3,C1QB,C1RL,C1S,C2,C3,C4A,C4B,CD1A,CD274,CD28,CD40,CD7,CD74,CD80,CEACAM1,CLEC10A,CLEC6A,CR1L,CSF2RB,CTLA4,CTSS,CX3CR1,ERAP2,EXO1,FGL1,GPR183,HLA-A,HLA-B,HLA-C,HLA-DMA,HLA-DMB,HLA-DOA,HLA-DOB,HLA-DPA1,HLA-DPB1,HLA-DQA1,HLA-DQB1,HLA-DQB2,HLA-DRA,HLA-DRB1,HLA-DRB5,HLA-E,HLA-F,HLA-H,ICAM1,IL12RB1,IL18BP,IL27,IL4I1,IRF1,IRF7,ITK,JAK2,JAK3,KLRK1,LAG3,LAMP3,LILRA1,LILRB3,MCOLN2,NOD2,P2RX7,PCYT1A,PDCD1,PDCD1LG2,RIPK2,RNF19B,RSAD2,SECTM1,SERPING1,SIT1,SLAMF1,SLAMF6,SLAMF7,SLC11A1,TAP1,TAP2,TBX21,TLR8,TNFRSF11A,TNFRSF21,TNFSF13B,TNFSF18,ZC3H12A
#> 2 B2M,HLA-DMA,HLA-DMB,HLA-DOA,HLA-DOB,HLA-DPA1,HLA-DPB1,HLA-DQA1,HLA-DQB1,HLA-DQB2,HLA-DRA,HLA-DRB1,HLA-DRB5
#> 3 B2M,CD74,CTSS,HLA-DMA,HLA-DMB,HLA-DOA,HLA-DOB,HLA-DPA1,HLA-DPB1,HLA-DQA1,HLA-DQB1,HLA-DQB2,HLA-DRA,HLA-DRB1,HLA-DRB5
#> 4 ACOD1,ADAM8,AIM2,APOBEC3A,APOBEC3D,APOBEC3G,APOL1,B2M,C1QB,C1RL,C1S,C2,C3,C4A,C4B,CALCOCO2,CALHM6,CASP4,CD274,CD300H,CD300LF,CD40,CD74,CEACAM1,CFB,CFH,CIITA,CLEC10A,CLEC6A,COLEC12,CTSS,CX3CR1,CXCL10,CYLD,DTX3L,EDN1,GBP1,GBP2,GBP3,GBP4,GBP5,GBP6,GBP7,GCH1,GSDMD,H2BC21,HLA-A,HLA-B,HLA-C,HLA-DPA1,HLA-E,HLA-F,IFI27,IFI35,IFIH1,IFIT2,IFIT3,IFITM1,IFITM2,IL12RB1,IL27,IRF1,IRF7,ISG20,JAK2,JAK3,KLRK1,LAG3,LILRA2,MCOLN2,MEFV,MSRB1,NCF1,NLRC5,NMI,NOD2,NUB1,OPTN,P2RX7,PIM1,PML,RAB20,RIPK2,RNF19B,RSAD2,SCIMP,SERPING1,SLAMF1,SLAMF6,SLAMF7,SLC11A1,STAT1,STAT2,TIFA,TLR10,TLR8,TRAFD1,TRIM17,TRIM22,TRIM69,UBD,UBE2L6,ZBP1,ZNFX1
#> 5 ACOD1,CALCOCO2,CD40,CD74,CIITA,EDN1,GBP1,GBP2,GBP3,GBP4,GBP5,GBP6,GBP7,GCH1,HLA-DPA1,IFITM1,IFITM2,IL12RB1,IRF1,JAK2,MEFV,NLRC5,NUB1,PIM1,RAB20,SLC11A1,STAT1,UBD
#> 6 B2M,CD1A,HLA-A,HLA-B,HLA-C,HLA-DRA,HLA-DRB1,HLA-E,HLA-F,HLA-H,IL12RB1,P2RX7,TAP2This will return a table with 9 columns. They contain:
GO.ID: The computer readable GO term ID.Term: The human readable GO term name.Annotated: The overall number of detected genes associated with this term (as defined in thede_containeror in thebg_genesparameters).Significant: The number of DE genes associated with this term (as defined in theres_deor in thede_genesparameters)Expected: The expected number of genes associated with this term.Rank in p.value_classic: specifies the rank of each term, if using the ascending order ofp.value_classicto sort the entries.p.value_elim: p-value for the enrichment test of each term (recommended for sorting the table), based on theelimalgorithm intopGO.p.value_classic: p-value for the enrichment, using the “classical” Fisher test.genes: Specifies which DE genes are associated with that term (separated by a comma). This column will later on be used to label the genes in thego_volcano()function (see below in Section 6.2)
mosdef and goseq
The method implemented in the goseq package is able to handle the selection bias inherent in assays such as RNA-seq, whereas highly expressed genes have a higher probability of being detected as differentially expressed.
Parameters like top_de, min_counts, verbose, FDR_threshold and de_type can also be used here (for more detail on these parameters see above), as they are a part of the shared API with run_topGO and run_cluPro.
Importantly, the feature length retrieval is based on the goseq() function, and this requires that the corresponding TxDb packages are installed and available. So make sure one is installed on your machine. For human samples, the recommended one is TxDb.Hsapiens.UCSC.hg38.knownGene.
goseq_macrophage <- run_goseq(
de_container = dds_macrophage,
res_de = res_macrophage_IFNg_vs_naive,
mapping = "org.Hs.eg.db",
testCats = "GO:BP" # which categories to test of ("GO:BP, "GO:MF", "GO:CC")
)
#> Your dataset has 1024 DE genes.
#> You selected 1024 (100.00%) genes for the enrichment analysis.
#> You are analyzing up_and_down-regulated genes in the `res_de` container
#> Can't find hg38/ensGene length data in genLenDataBase...
#> Warning in grep(txdbPattern, installedPackages): argument 'pattern' has length
#> > 1 and only the first element will be used
#> Found the annotation package, TxDb.Hsapiens.UCSC.hg38.knownGene
#> Trying to get the gene lengths from it.
#> Loading required package: GenomicFeatures
#>
#> Attaching package: 'GenomicFeatures'
#> The following object is masked from 'package:topGO':
#>
#> genes
#> Warning in pcls(G): initial point very close to some inequality constraints
#> Fetching GO annotations...
#> For 3710 genes, we could not find any categories. These genes will be excluded.
#> To force their use, please run with use_genes_without_cat=TRUE (see documentation).
#> This was the default behavior for version 1.15.1 and earlier.
#> Calculating the p-values...
#> 'select()' returned 1:1 mapping between keys and columns
#> 'select()' returned 1:many mapping between keys and columns
head(goseq_macrophage)
#> category over_represented_pvalue under_represented_pvalue numDEInCat
#> 1766 GO:0006955 4.037493e-55 1 240
#> 610 GO:0002376 1.618960e-49 1 291
#> 523 GO:0002250 4.897194e-41 1 104
#> 2392 GO:0009607 1.552951e-39 1 197
#> 8181 GO:0051707 2.869334e-39 1 193
#> 6262 GO:0043207 3.258071e-39 1 193
#> numInCat term ontology p.adj
#> 1766 1427 immune response BP 5.854365e-51
#> 610 2102 immune system process BP 1.173746e-45
#> 523 385 adaptive immune response BP 2.366977e-37
#> 2392 1257 response to biotic stimulus BP 5.629447e-36
#> 8181 1220 response to other organism BP 7.873671e-36
#> 6262 1221 response to external biotic stimulus BP 7.873671e-36
#> genes
#> 1766 ENSG00000125347,ENSG00000162645,ENSG00000145365,ENSG00000137496,ENSG00000154451,ENSG00000231389,ENSG00000204257,ENSG00000100342,ENSG00000162654,ENSG00000164509,ENSG00000204267,ENSG00000131203,ENSG00000213886,ENSG00000168394,ENSG00000242574,ENSG00000163568,ENSG00000183734,ENSG00000101017,ENSG00000117228,ENSG00000244731,ENSG00000019582,ENSG00000204252,ENSG00000089041,ENSG00000179583,ENSG00000136436,ENSG00000188820,ENSG00000120217,ENSG00000204287,ENSG00000131979,ENSG00000096996,ENSG00000113263,ENSG00000169248,ENSG00000117226,ENSG00000026751,ENSG00000224389,ENSG00000004468,ENSG00000197646,ENSG00000164136,ENSG00000149131,ENSG00000008517,ENSG00000089692,ENSG00000184588,ENSG00000078081,ENSG00000223865,ENSG00000073861,ENSG00000164308,ENSG00000173369,ENSG00000169245,ENSG00000196126,ENSG00000167207,ENSG00000204642,ENSG00000079385,ENSG00000123146,ENSG00000179344,ENSG00000181374,ENSG00000186470,ENSG00000198502,ENSG00000234745,ENSG00000000971,ENSG00000152207,ENSG00000213809,ENSG00000140853,ENSG00000121858,ENSG00000243649,ENSG00000026950,ENSG00000206341,ENSG00000204592,ENSG00000102794,ENSG00000141574,ENSG00000153064,ENSG00000138755,ENSG00000172183,ENSG00000141655,ENSG00000206503,ENSG00000123609,ENSG00000123240,ENSG00000115415,ENSG00000213512,ENSG00000163599,ENSG00000162931,ENSG00000204525,ENSG00000198736,ENSG00000096968,ENSG00000198829,ENSG00000168329,ENSG00000205220,ENSG00000127951,ENSG00000013374,ENSG00000151651,ENSG00000137193,ENSG00000135148,ENSG00000232629,ENSG00000158270,ENSG00000197721,ENSG00000165949,ENSG00000173762,ENSG00000104312,ENSG00000101916,ENSG00000156587,ENSG00000111801,ENSG00000104951,ENSG00000166278,ENSG00000102524,ENSG00000018280,ENSG00000170581,ENSG00000108688,ENSG00000169508,ENSG00000197272,ENSG00000026103,ENSG00000068079,ENSG00000140749,ENSG00000178562,ENSG00000153898,ENSG00000241106,ENSG00000196735,ENSG00000185201,ENSG00000090339,ENSG00000284690,ENSG00000205846,ENSG00000275718,ENSG00000243811,ENSG00000124256,ENSG00000204577,ENSG00000184678,ENSG00000185885,ENSG00000120337,ENSG00000121594,ENSG00000104518,ENSG00000188389,ENSG00000132274,ENSG00000140464,ENSG00000100368,ENSG00000146072,ENSG00000116514,ENSG00000166710,ENSG00000108700,ENSG00000128383,ENSG00000125730,ENSG00000162739,ENSG00000239713,ENSG00000132514,ENSG00000186074,ENSG00000103313,ENSG00000161929,ENSG00000189171,ENSG00000119917,ENSG00000174123,ENSG00000163874,ENSG00000121797,ENSG00000163131,ENSG00000105639,ENSG00000083799,ENSG00000104760,ENSG00000203805,ENSG00000119922,ENSG00000196954,ENSG00000035720,ENSG00000158477,ENSG00000124201,ENSG00000139832,ENSG00000174371,ENSG00000185507,ENSG00000185880,ENSG00000134321,ENSG00000104974,ENSG00000120436,ENSG00000137959,ENSG00000136960,ENSG00000173198,ENSG00000124508,ENSG00000182326,ENSG00000078401,ENSG00000139178,ENSG00000115267,ENSG00000100226,ENSG00000137078,ENSG00000117090,ENSG00000158517,ENSG00000163840,ENSG00000183347,ENSG00000113749,ENSG00000239998,ENSG00000186810,ENSG00000136689,ENSG00000161217,ENSG00000064932,ENSG00000054219,ENSG00000204616,ENSG00000137628,ENSG00000135636,ENSG00000159403,ENSG00000142089,ENSG00000110848,ENSG00000065427,ENSG00000075240,ENSG00000204632,ENSG00000082074,ENSG00000158714,ENSG00000158481,ENSG00000158813,ENSG00000187554,ENSG00000171522,ENSG00000237541,ENSG00000099985,ENSG00000104856,ENSG00000113916,ENSG00000275385,ENSG00000189067,ENSG00000178999,ENSG00000271503,ENSG00000254087,ENSG00000106952,ENSG00000168811,ENSG00000111335,ENSG00000163735,ENSG00000255833,ENSG00000163564,ENSG00000152778,ENSG00000164300,ENSG00000136044,ENSG00000173193,ENSG00000198719,ENSG00000196664,ENSG00000085265,ENSG00000243414,ENSG00000076248,ENSG00000184371,ENSG00000226979,ENSG00000119508,ENSG00000157873,ENSG00000136560,ENSG00000041880,ENSG00000111331,ENSG00000138496,ENSG00000104432,ENSG00000135047,ENSG00000092445,ENSG00000188313,ENSG00000112149,ENSG00000137265
#> 610 ENSG00000125347,ENSG00000162645,ENSG00000145365,ENSG00000137496,ENSG00000154451,ENSG00000231389,ENSG00000204257,ENSG00000100342,ENSG00000162654,ENSG00000134470,ENSG00000164509,ENSG00000204267,ENSG00000131203,ENSG00000213886,ENSG00000168394,ENSG00000242574,ENSG00000163568,ENSG00000183734,ENSG00000101017,ENSG00000117228,ENSG00000244731,ENSG00000019582,ENSG00000204252,ENSG00000089041,ENSG00000179583,ENSG00000136436,ENSG00000170989,ENSG00000185338,ENSG00000188820,ENSG00000120217,ENSG00000188906,ENSG00000204287,ENSG00000131979,ENSG00000096996,ENSG00000113263,ENSG00000169248,ENSG00000117226,ENSG00000026751,ENSG00000240065,ENSG00000224389,ENSG00000004468,ENSG00000197646,ENSG00000164136,ENSG00000149131,ENSG00000008517,ENSG00000089692,ENSG00000184588,ENSG00000078081,ENSG00000223865,ENSG00000073861,ENSG00000164308,ENSG00000173369,ENSG00000169245,ENSG00000196126,ENSG00000167207,ENSG00000110852,ENSG00000204642,ENSG00000079385,ENSG00000123146,ENSG00000179344,ENSG00000181374,ENSG00000186470,ENSG00000198502,ENSG00000234745,ENSG00000000971,ENSG00000152207,ENSG00000188404,ENSG00000213809,ENSG00000140853,ENSG00000121858,ENSG00000092010,ENSG00000243649,ENSG00000026950,ENSG00000206341,ENSG00000204592,ENSG00000102794,ENSG00000141574,ENSG00000168062,ENSG00000153064,ENSG00000138755,ENSG00000172183,ENSG00000141655,ENSG00000206503,ENSG00000123609,ENSG00000188676,ENSG00000117115,ENSG00000123240,ENSG00000115415,ENSG00000213512,ENSG00000163599,ENSG00000162931,ENSG00000204525,ENSG00000182782,ENSG00000198736,ENSG00000096968,ENSG00000198829,ENSG00000168329,ENSG00000205220,ENSG00000127951,ENSG00000013374,ENSG00000002933,ENSG00000151651,ENSG00000137193,ENSG00000135148,ENSG00000135424,ENSG00000232629,ENSG00000158270,ENSG00000197721,ENSG00000106565,ENSG00000165949,ENSG00000173762,ENSG00000088992,ENSG00000104312,ENSG00000101916,ENSG00000156587,ENSG00000111801,ENSG00000104951,ENSG00000123685,ENSG00000166278,ENSG00000102524,ENSG00000018280,ENSG00000170581,ENSG00000182580,ENSG00000108688,ENSG00000169508,ENSG00000231925,ENSG00000197272,ENSG00000026103,ENSG00000204264,ENSG00000068079,ENSG00000140749,ENSG00000178562,ENSG00000153898,ENSG00000241106,ENSG00000196735,ENSG00000162692,ENSG00000185201,ENSG00000090339,ENSG00000049130,ENSG00000099377,ENSG00000284690,ENSG00000153094,ENSG00000205846,ENSG00000275718,ENSG00000243811,ENSG00000124256,ENSG00000204577,ENSG00000184678,ENSG00000185885,ENSG00000090554,ENSG00000120337,ENSG00000121594,ENSG00000104518,ENSG00000188389,ENSG00000162367,ENSG00000116016,ENSG00000064201,ENSG00000132274,ENSG00000140464,ENSG00000100368,ENSG00000146072,ENSG00000116514,ENSG00000173821,ENSG00000166710,ENSG00000108700,ENSG00000128383,ENSG00000125730,ENSG00000162739,ENSG00000239713,ENSG00000132514,ENSG00000186074,ENSG00000103313,ENSG00000161929,ENSG00000189171,ENSG00000119917,ENSG00000174123,ENSG00000163874,ENSG00000121797,ENSG00000163131,ENSG00000105639,ENSG00000083799,ENSG00000104760,ENSG00000135124,ENSG00000133800,ENSG00000203805,ENSG00000119922,ENSG00000196954,ENSG00000023330,ENSG00000035720,ENSG00000158477,ENSG00000124201,ENSG00000139832,ENSG00000174371,ENSG00000006747,ENSG00000185507,ENSG00000119969,ENSG00000185880,ENSG00000134321,ENSG00000125810,ENSG00000162337,ENSG00000104974,ENSG00000120436,ENSG00000137959,ENSG00000136960,ENSG00000173198,ENSG00000170271,ENSG00000124508,ENSG00000182326,ENSG00000078401,ENSG00000139178,ENSG00000150630,ENSG00000115267,ENSG00000100226,ENSG00000137078,ENSG00000117090,ENSG00000158517,ENSG00000163840,ENSG00000183347,ENSG00000141682,ENSG00000113749,ENSG00000239998,ENSG00000186810,ENSG00000134256,ENSG00000136689,ENSG00000161217,ENSG00000139192,ENSG00000064932,ENSG00000054219,ENSG00000204616,ENSG00000137628,ENSG00000135636,ENSG00000159403,ENSG00000154639,ENSG00000142089,ENSG00000110848,ENSG00000065427,ENSG00000075240,ENSG00000204632,ENSG00000100628,ENSG00000082074,ENSG00000158714,ENSG00000070501,ENSG00000158481,ENSG00000158813,ENSG00000187554,ENSG00000146918,ENSG00000171522,ENSG00000237541,ENSG00000099985,ENSG00000104856,ENSG00000113916,ENSG00000275385,ENSG00000189067,ENSG00000178999,ENSG00000271503,ENSG00000254087,ENSG00000106952,ENSG00000168811,ENSG00000196684,ENSG00000111335,ENSG00000163735,ENSG00000255833,ENSG00000163564,ENSG00000152778,ENSG00000164300,ENSG00000123610,ENSG00000136044,ENSG00000173193,ENSG00000198719,ENSG00000196664,ENSG00000085265,ENSG00000142405,ENSG00000243414,ENSG00000076248,ENSG00000184371,ENSG00000226979,ENSG00000113249,ENSG00000119508,ENSG00000157873,ENSG00000136560,ENSG00000041880,ENSG00000111331,ENSG00000138496,ENSG00000153208,ENSG00000104432,ENSG00000135047,ENSG00000129422,ENSG00000092445,ENSG00000188313,ENSG00000112149,ENSG00000137265
#> 523 ENSG00000125347,ENSG00000137496,ENSG00000231389,ENSG00000204257,ENSG00000204267,ENSG00000168394,ENSG00000242574,ENSG00000183734,ENSG00000101017,ENSG00000244731,ENSG00000019582,ENSG00000204252,ENSG00000089041,ENSG00000120217,ENSG00000204287,ENSG00000096996,ENSG00000113263,ENSG00000026751,ENSG00000224389,ENSG00000197646,ENSG00000149131,ENSG00000089692,ENSG00000078081,ENSG00000223865,ENSG00000073861,ENSG00000164308,ENSG00000173369,ENSG00000196126,ENSG00000167207,ENSG00000204642,ENSG00000079385,ENSG00000179344,ENSG00000186470,ENSG00000198502,ENSG00000234745,ENSG00000213809,ENSG00000026950,ENSG00000206341,ENSG00000204592,ENSG00000141574,ENSG00000141655,ENSG00000206503,ENSG00000163599,ENSG00000204525,ENSG00000096968,ENSG00000168329,ENSG00000232629,ENSG00000197721,ENSG00000173762,ENSG00000104312,ENSG00000101916,ENSG00000111801,ENSG00000104951,ENSG00000166278,ENSG00000102524,ENSG00000018280,ENSG00000169508,ENSG00000197272,ENSG00000178562,ENSG00000153898,ENSG00000241106,ENSG00000196735,ENSG00000090339,ENSG00000205846,ENSG00000204577,ENSG00000120337,ENSG00000121594,ENSG00000188389,ENSG00000100368,ENSG00000146072,ENSG00000116514,ENSG00000166710,ENSG00000125730,ENSG00000162739,ENSG00000132514,ENSG00000163874,ENSG00000163131,ENSG00000105639,ENSG00000104760,ENSG00000158477,ENSG00000174371,ENSG00000185507,ENSG00000134321,ENSG00000104974,ENSG00000182326,ENSG00000139178,ENSG00000137078,ENSG00000117090,ENSG00000161217,ENSG00000159403,ENSG00000110848,ENSG00000204632,ENSG00000158481,ENSG00000237541,ENSG00000104856,ENSG00000113916,ENSG00000254087,ENSG00000168811,ENSG00000076248,ENSG00000226979,ENSG00000157873,ENSG00000041880,ENSG00000135047,ENSG00000137265
#> 2392 ENSG00000125347,ENSG00000162645,ENSG00000145365,ENSG00000137496,ENSG00000154451,ENSG00000231389,ENSG00000100342,ENSG00000162654,ENSG00000164509,ENSG00000204267,ENSG00000131203,ENSG00000213886,ENSG00000163568,ENSG00000101017,ENSG00000117228,ENSG00000244731,ENSG00000019582,ENSG00000089041,ENSG00000179583,ENSG00000136436,ENSG00000188820,ENSG00000120217,ENSG00000131979,ENSG00000096996,ENSG00000169248,ENSG00000117226,ENSG00000026751,ENSG00000224389,ENSG00000197646,ENSG00000164136,ENSG00000149131,ENSG00000186439,ENSG00000089692,ENSG00000184588,ENSG00000073861,ENSG00000173369,ENSG00000169245,ENSG00000196126,ENSG00000167207,ENSG00000204642,ENSG00000079385,ENSG00000181374,ENSG00000234745,ENSG00000000971,ENSG00000213809,ENSG00000140853,ENSG00000243649,ENSG00000204592,ENSG00000102794,ENSG00000168062,ENSG00000153064,ENSG00000138755,ENSG00000172183,ENSG00000141655,ENSG00000206503,ENSG00000123609,ENSG00000123240,ENSG00000115415,ENSG00000213512,ENSG00000162931,ENSG00000204525,ENSG00000198736,ENSG00000096968,ENSG00000168329,ENSG00000127951,ENSG00000013374,ENSG00000151651,ENSG00000137193,ENSG00000135148,ENSG00000178726,ENSG00000158270,ENSG00000165949,ENSG00000104312,ENSG00000176485,ENSG00000101916,ENSG00000156587,ENSG00000104951,ENSG00000123685,ENSG00000166278,ENSG00000018280,ENSG00000170581,ENSG00000108688,ENSG00000197272,ENSG00000101412,ENSG00000068079,ENSG00000153898,ENSG00000162692,ENSG00000140465,ENSG00000185201,ENSG00000284690,ENSG00000136514,ENSG00000136826,ENSG00000205846,ENSG00000275718,ENSG00000243811,ENSG00000124256,ENSG00000184678,ENSG00000185885,ENSG00000121594,ENSG00000104518,ENSG00000188389,ENSG00000064201,ENSG00000132274,ENSG00000140464,ENSG00000108950,ENSG00000100368,ENSG00000116514,ENSG00000173821,ENSG00000166710,ENSG00000108700,ENSG00000128383,ENSG00000125730,ENSG00000162739,ENSG00000239713,ENSG00000132514,ENSG00000186074,ENSG00000103313,ENSG00000161929,ENSG00000119917,ENSG00000174123,ENSG00000163874,ENSG00000163131,ENSG00000167914,ENSG00000105639,ENSG00000083799,ENSG00000119922,ENSG00000196954,ENSG00000035720,ENSG00000124201,ENSG00000139832,ENSG00000185507,ENSG00000204397,ENSG00000185880,ENSG00000165806,ENSG00000081985,ENSG00000134321,ENSG00000120436,ENSG00000100985,ENSG00000137959,ENSG00000182326,ENSG00000078401,ENSG00000139178,ENSG00000115267,ENSG00000166920,ENSG00000117090,ENSG00000158517,ENSG00000163840,ENSG00000183347,ENSG00000141682,ENSG00000239998,ENSG00000064932,ENSG00000204616,ENSG00000137628,ENSG00000159403,ENSG00000154639,ENSG00000142089,ENSG00000167992,ENSG00000075240,ENSG00000204632,ENSG00000158714,ENSG00000125355,ENSG00000187554,ENSG00000171522,ENSG00000104856,ENSG00000175175,ENSG00000275385,ENSG00000134326,ENSG00000189067,ENSG00000178999,ENSG00000271503,ENSG00000254087,ENSG00000106952,ENSG00000168811,ENSG00000111335,ENSG00000163735,ENSG00000255833,ENSG00000163564,ENSG00000152778,ENSG00000117632,ENSG00000164300,ENSG00000136044,ENSG00000173193,ENSG00000196664,ENSG00000085265,ENSG00000243414,ENSG00000184371,ENSG00000226979,ENSG00000175445,ENSG00000154920,ENSG00000157873,ENSG00000136560,ENSG00000111331,ENSG00000114698,ENSG00000138496,ENSG00000092445,ENSG00000188313,ENSG00000137265
#> 8181 ENSG00000125347,ENSG00000162645,ENSG00000145365,ENSG00000137496,ENSG00000154451,ENSG00000231389,ENSG00000100342,ENSG00000162654,ENSG00000164509,ENSG00000204267,ENSG00000131203,ENSG00000213886,ENSG00000163568,ENSG00000101017,ENSG00000117228,ENSG00000244731,ENSG00000019582,ENSG00000089041,ENSG00000179583,ENSG00000136436,ENSG00000188820,ENSG00000120217,ENSG00000131979,ENSG00000096996,ENSG00000169248,ENSG00000117226,ENSG00000026751,ENSG00000224389,ENSG00000197646,ENSG00000164136,ENSG00000149131,ENSG00000186439,ENSG00000089692,ENSG00000184588,ENSG00000073861,ENSG00000173369,ENSG00000169245,ENSG00000196126,ENSG00000167207,ENSG00000204642,ENSG00000079385,ENSG00000181374,ENSG00000234745,ENSG00000000971,ENSG00000213809,ENSG00000140853,ENSG00000243649,ENSG00000204592,ENSG00000102794,ENSG00000168062,ENSG00000153064,ENSG00000138755,ENSG00000172183,ENSG00000141655,ENSG00000206503,ENSG00000123609,ENSG00000123240,ENSG00000115415,ENSG00000213512,ENSG00000162931,ENSG00000204525,ENSG00000198736,ENSG00000096968,ENSG00000168329,ENSG00000127951,ENSG00000013374,ENSG00000151651,ENSG00000137193,ENSG00000135148,ENSG00000178726,ENSG00000158270,ENSG00000165949,ENSG00000104312,ENSG00000176485,ENSG00000101916,ENSG00000156587,ENSG00000123685,ENSG00000166278,ENSG00000018280,ENSG00000170581,ENSG00000108688,ENSG00000197272,ENSG00000101412,ENSG00000068079,ENSG00000153898,ENSG00000162692,ENSG00000140465,ENSG00000185201,ENSG00000284690,ENSG00000136514,ENSG00000205846,ENSG00000275718,ENSG00000243811,ENSG00000124256,ENSG00000184678,ENSG00000185885,ENSG00000121594,ENSG00000104518,ENSG00000064201,ENSG00000132274,ENSG00000140464,ENSG00000108950,ENSG00000100368,ENSG00000116514,ENSG00000173821,ENSG00000166710,ENSG00000108700,ENSG00000128383,ENSG00000125730,ENSG00000162739,ENSG00000239713,ENSG00000132514,ENSG00000186074,ENSG00000103313,ENSG00000161929,ENSG00000119917,ENSG00000174123,ENSG00000163874,ENSG00000163131,ENSG00000167914,ENSG00000105639,ENSG00000083799,ENSG00000119922,ENSG00000196954,ENSG00000035720,ENSG00000124201,ENSG00000139832,ENSG00000185507,ENSG00000204397,ENSG00000185880,ENSG00000165806,ENSG00000081985,ENSG00000134321,ENSG00000120436,ENSG00000100985,ENSG00000137959,ENSG00000182326,ENSG00000078401,ENSG00000139178,ENSG00000115267,ENSG00000166920,ENSG00000117090,ENSG00000158517,ENSG00000163840,ENSG00000183347,ENSG00000141682,ENSG00000239998,ENSG00000064932,ENSG00000204616,ENSG00000137628,ENSG00000159403,ENSG00000154639,ENSG00000142089,ENSG00000167992,ENSG00000075240,ENSG00000204632,ENSG00000158714,ENSG00000125355,ENSG00000187554,ENSG00000171522,ENSG00000104856,ENSG00000175175,ENSG00000275385,ENSG00000134326,ENSG00000189067,ENSG00000178999,ENSG00000271503,ENSG00000254087,ENSG00000106952,ENSG00000168811,ENSG00000111335,ENSG00000163735,ENSG00000255833,ENSG00000163564,ENSG00000152778,ENSG00000117632,ENSG00000164300,ENSG00000136044,ENSG00000173193,ENSG00000196664,ENSG00000085265,ENSG00000243414,ENSG00000184371,ENSG00000226979,ENSG00000175445,ENSG00000157873,ENSG00000136560,ENSG00000111331,ENSG00000114698,ENSG00000138496,ENSG00000092445,ENSG00000188313,ENSG00000137265
#> 6262 ENSG00000125347,ENSG00000162645,ENSG00000145365,ENSG00000137496,ENSG00000154451,ENSG00000231389,ENSG00000100342,ENSG00000162654,ENSG00000164509,ENSG00000204267,ENSG00000131203,ENSG00000213886,ENSG00000163568,ENSG00000101017,ENSG00000117228,ENSG00000244731,ENSG00000019582,ENSG00000089041,ENSG00000179583,ENSG00000136436,ENSG00000188820,ENSG00000120217,ENSG00000131979,ENSG00000096996,ENSG00000169248,ENSG00000117226,ENSG00000026751,ENSG00000224389,ENSG00000197646,ENSG00000164136,ENSG00000149131,ENSG00000186439,ENSG00000089692,ENSG00000184588,ENSG00000073861,ENSG00000173369,ENSG00000169245,ENSG00000196126,ENSG00000167207,ENSG00000204642,ENSG00000079385,ENSG00000181374,ENSG00000234745,ENSG00000000971,ENSG00000213809,ENSG00000140853,ENSG00000243649,ENSG00000204592,ENSG00000102794,ENSG00000168062,ENSG00000153064,ENSG00000138755,ENSG00000172183,ENSG00000141655,ENSG00000206503,ENSG00000123609,ENSG00000123240,ENSG00000115415,ENSG00000213512,ENSG00000162931,ENSG00000204525,ENSG00000198736,ENSG00000096968,ENSG00000168329,ENSG00000127951,ENSG00000013374,ENSG00000151651,ENSG00000137193,ENSG00000135148,ENSG00000178726,ENSG00000158270,ENSG00000165949,ENSG00000104312,ENSG00000176485,ENSG00000101916,ENSG00000156587,ENSG00000123685,ENSG00000166278,ENSG00000018280,ENSG00000170581,ENSG00000108688,ENSG00000197272,ENSG00000101412,ENSG00000068079,ENSG00000153898,ENSG00000162692,ENSG00000140465,ENSG00000185201,ENSG00000284690,ENSG00000136514,ENSG00000205846,ENSG00000275718,ENSG00000243811,ENSG00000124256,ENSG00000184678,ENSG00000185885,ENSG00000121594,ENSG00000104518,ENSG00000064201,ENSG00000132274,ENSG00000140464,ENSG00000108950,ENSG00000100368,ENSG00000116514,ENSG00000173821,ENSG00000166710,ENSG00000108700,ENSG00000128383,ENSG00000125730,ENSG00000162739,ENSG00000239713,ENSG00000132514,ENSG00000186074,ENSG00000103313,ENSG00000161929,ENSG00000119917,ENSG00000174123,ENSG00000163874,ENSG00000163131,ENSG00000167914,ENSG00000105639,ENSG00000083799,ENSG00000119922,ENSG00000196954,ENSG00000035720,ENSG00000124201,ENSG00000139832,ENSG00000185507,ENSG00000204397,ENSG00000185880,ENSG00000165806,ENSG00000081985,ENSG00000134321,ENSG00000120436,ENSG00000100985,ENSG00000137959,ENSG00000182326,ENSG00000078401,ENSG00000139178,ENSG00000115267,ENSG00000166920,ENSG00000117090,ENSG00000158517,ENSG00000163840,ENSG00000183347,ENSG00000141682,ENSG00000239998,ENSG00000064932,ENSG00000204616,ENSG00000137628,ENSG00000159403,ENSG00000154639,ENSG00000142089,ENSG00000167992,ENSG00000075240,ENSG00000204632,ENSG00000158714,ENSG00000125355,ENSG00000187554,ENSG00000171522,ENSG00000104856,ENSG00000175175,ENSG00000275385,ENSG00000134326,ENSG00000189067,ENSG00000178999,ENSG00000271503,ENSG00000254087,ENSG00000106952,ENSG00000168811,ENSG00000111335,ENSG00000163735,ENSG00000255833,ENSG00000163564,ENSG00000152778,ENSG00000117632,ENSG00000164300,ENSG00000136044,ENSG00000173193,ENSG00000196664,ENSG00000085265,ENSG00000243414,ENSG00000184371,ENSG00000226979,ENSG00000175445,ENSG00000157873,ENSG00000136560,ENSG00000111331,ENSG00000114698,ENSG00000138496,ENSG00000092445,ENSG00000188313,ENSG00000137265
#> genesymbols
#> 1766 ACOD1,ADAM8,ADGRE5,AIM2,APOBEC3A,APOBEC3D,APOBEC3G,APOL1,APPL2,ASCL2,AURKB,B2M,BANK1,BCL6,BTN2A2,BTN3A1,BTN3A2,BTN3A3,C1QB,C1R,C1RL,C1S,C2,C3,C4A,C4B,CALCOCO2,CALHM6,CASP4,CCL13,CCL15,CCL18,CCL5,CCL7,CCL8,CCRL2,CD1A,CD1C,CD274,CD28,CD300H,CD300LF,CD38,CD40,CD69,CD7,CD74,CD80,CD83,CEACAM1,CFB,CFH,CIITA,CLEC10A,CLEC6A,COLEC12,CR1L,CSF1,CSF2RB,CTLA4,CTSL,CTSS,CX3CR1,CXCL10,CXCL11,CXCL5,CXCL9,CXCR3,CYLD,CYSLTR1,CYSLTR2,DDX60,DLL1,DTX3L,DYSF,EDA,EDN1,ENPP2,ERAP2,EXO1,FAS,FCN1,FGL1,FGL2,FYB1,GBP1,GBP2,GBP3,GBP4,GBP5,GBP6,GBP7,GCH1,GPR183,GPR31,GRAMD4,GSDMD,GTPBP1,H2BC21,HLA-A,HLA-B,HLA-C,HLA-DMA,HLA-DMB,HLA-DOA,HLA-DOB,HLA-DPA1,HLA-DPB1,HLA-DQA1,HLA-DQA1,HLA-DQB1,HLA-DQB2,HLA-DRA,HLA-DRB1,HLA-DRB5,HLA-E,HLA-F,HLA-G,HLA-H,HRH2,ICAM1,IDO1,IFI27,IFI35,IFI44L,IFIH1,IFIT2,IFIT3,IFIT5,IFITM1,IFITM2,IFITM3,IGSF6,IL12A,IL12RB1,IL15,IL18BP,IL1RN,IL27,IL31RA,IL32,IL4I1,IL7,IRF1,IRF4,IRF7,ISG20,ITK,JAK2,JAK3,KARS1,KLRK1,LAG3,LAMP3,LILRA1,LILRA2,LILRB3,LITAF,LTA,LY75,LYN,MCOLN2,MEFV,MSRB1,NCF1,NLRC5,NMI,NOD2,NR4A3,NUB1,OAS2,OAS3,OPTN,OSM,P2RX7,PARP14,PARP3,PARP9,PCYT1A,PDCD1,PDCD1LG2,PDE4B,PIM1,PLPP4,PLSCR1,PML,PSMB10,PTGER4,PYHIN1,RAB20,RELB,RIPK2,RNF19B,RSAD2,S100A13,SBNO2,SCIMP,SECTM1,SERINC5,SERPING1,SIT1,SLAMF1,SLAMF6,SLAMF7,SLAMF8,SLC11A1,STAP1,STAT1,STAT2,SUCNR1,TANK,TAP1,TAP2,TBX21,TICAM2,TIFA,TIFAB,TLR10,TLR5,TLR7,TLR8,TNFRSF11A,TNFRSF14,TNFRSF21,TNFSF10,TNFSF13B,TNFSF18,TNFSF8,TRAFD1,TRIM17,TRIM22,TRIM31,TRIM69,TYRO3,UBD,UBE2L6,UNG,ZBP1,ZC3H12A,ZNFX1
#> 610 ACOD1,ADAM8,ADGRE5,AIM2,ALAS1,APOBEC3A,APOBEC3D,APOBEC3G,APOL1,APPL2,ASB2,ASCL2,AURKB,B2M,BANK1,BATF2,BATF3,BCL2L11,BCL6,BTN2A2,BTN3A1,BTN3A2,BTN3A3,C1QB,C1R,C1RL,C1S,C2,C3,C4A,C4B,CALCOCO2,CALHM6,CASP4,CCL13,CCL15,CCL18,CCL5,CCL7,CCL8,CCRL2,CD101,CD1A,CD1C,CD274,CD28,CD300H,CD300LF,CD38,CD40,CD69,CD7,CD74,CD80,CD83,CD93,CEACAM1,CFB,CFH,CIITA,CLEC10A,CLEC2B,CLEC6A,COLEC12,CR1L,CSF1,CSF2RB,CTLA4,CTSL,CTSS,CX3CR1,CXADR,CXCL10,CXCL11,CXCL5,CXCL9,CXCR3,CYLD,CYSLTR1,CYSLTR2,DDX60,DLL1,DTX3L,DYSF,EDA,EDN1,ENPP2,EPAS1,EPHB3,ERAP2,EXO1,FAS,FAXDC2,FCN1,FGL1,FGL2,FLT3LG,FYB1,GBP1,GBP2,GBP3,GBP4,GBP5,GBP6,GBP7,GCH1,GPR183,GPR31,GRAMD4,GSDMD,GTPBP1,H2BC21,HAVCR1,HCAR2,HELLS,HLA-A,HLA-B,HLA-C,HLA-DMA,HLA-DMB,HLA-DOA,HLA-DOB,HLA-DPA1,HLA-DPB1,HLA-DQA1,HLA-DQA1,HLA-DQB1,HLA-DQB2,HLA-DRA,HLA-DRB1,HLA-DRB5,HLA-E,HLA-F,HLA-G,HLA-H,HRH2,HSD3B7,HSH2D,ICAM1,IDO1,IDO2,IFI27,IFI35,IFI44L,IFIH1,IFIT2,IFIT3,IFIT5,IFITM1,IFITM2,IFITM3,IGSF6,IL12A,IL12RB1,IL15,IL15RA,IL18BP,IL1RN,IL27,IL31RA,IL32,IL4I1,IL7,IRF1,IRF4,IRF7,ISG20,ITGA7,ITK,JAK2,JAK3,KARS1,KITLG,KLRK1,LAG3,LAMP3,LILRA1,LILRA2,LILRB3,LITAF,LRP5,LRRK2,LTA,LY75,LYN,LYVE1,MCOLN2,MEFV,MERTK,MSRB1,MTUS1,NCAPG2,NCF1,NLRC5,NLRP12,NMI,NOD2,NR4A3,NUB1,OAS2,OAS3,OPTN,OSM,P2RX4,P2RX7,PADI2,PARP14,PARP3,PARP9,PCYT1A,PDCD1,PDCD1LG2,PDE4B,PIM1,PLPP4,PLSCR1,PMAIP1,PML,POLB,PSMB10,PSMB8,PSMB9,PSME1,PTGER4,PYHIN1,RAB20,RELB,RIPK2,RNF19B,RNF213,RSAD2,S100A13,S1PR1,SBNO2,SCIMP,SCIN,SECTM1,SELL,SERINC5,SERPING1,SIT1,SLAMF1,SLAMF6,SLAMF7,SLAMF8,SLC11A1,SOCS1,STAP1,STAT1,STAT2,SUCNR1,TAL1,TANK,TAP1,TAP2,TAPBP,TAPBPL,TBX21,TESC,TICAM2,TIFA,TIFAB,TLR10,TLR5,TLR7,TLR8,TMEM176A,TMEM176B,TNFAIP6,TNFRSF11A,TNFRSF14,TNFRSF21,TNFSF10,TNFSF13B,TNFSF18,TNFSF8,TRAFD1,TRIM17,TRIM22,TRIM31,TRIM69,TSPAN32,TYRO3,UBD,UBE2L6,UNG,VCAM1,VEGFC,ZBP1,ZC3H12A,ZNFX1
#> 523 ASCL2,B2M,BCL6,BTN3A1,BTN3A2,BTN3A3,C1QB,C1R,C1RL,C1S,C2,C3,C4A,C4B,CD1A,CD1C,CD274,CD28,CD40,CD69,CD7,CD74,CD80,CEACAM1,CLEC10A,CLEC6A,CR1L,CSF2RB,CTLA4,CTSL,CTSS,CX3CR1,ERAP2,EXO1,FGL1,GPR183,HLA-A,HLA-B,HLA-C,HLA-DMA,HLA-DMB,HLA-DOA,HLA-DOB,HLA-DPA1,HLA-DPB1,HLA-DQA1,HLA-DQA1,HLA-DQB1,HLA-DQB2,HLA-DRA,HLA-DRB1,HLA-DRB5,HLA-E,HLA-F,HLA-G,HLA-H,ICAM1,IL12A,IL12RB1,IL18BP,IL27,IL4I1,IRF1,IRF4,IRF7,ITK,JAK2,JAK3,KLRK1,LAG3,LAMP3,LILRA1,LILRB3,LTA,LYN,MCOLN2,NOD2,P2RX7,PARP3,PCYT1A,PDCD1,PDCD1LG2,RELB,RIPK2,RNF19B,RSAD2,SECTM1,SERPING1,SIT1,SLAMF1,SLAMF6,SLAMF7,SLC11A1,TAP1,TAP2,TBX21,TLR8,TNFRSF11A,TNFRSF14,TNFRSF21,TNFSF13B,TNFSF18,UNG,ZC3H12A
#> 2392 ACOD1,ADAM8,AIM2,APOBEC3A,APOBEC3D,APOBEC3G,APOL1,APPL2,AURKB,B2M,BANK1,BATF2,BATF3,C15orf48,C1QB,C1R,C1RL,C1S,C2,C3,C4A,C4B,CALCOCO2,CALHM6,CARD16,CASP4,CASP7,CCL13,CCL15,CCL18,CCL5,CCL7,CCL8,CD274,CD300H,CD300LF,CD40,CD74,CD80,CEACAM1,CFB,CFH,CIITA,CLEC10A,CLEC6A,CMPK2,COLEC12,CSF1,CSF2RB,CTSS,CX3CR1,CXADR,CXCL10,CXCL11,CXCL5,CXCL9,CYLD,CYP1A1,DDX60,DTX3L,E2F1,EDN1,EME1,FAM20A,FCN1,FGL2,GBP1,GBP2,GBP3,GBP4,GBP5,GBP6,GBP7,GCH1,GPR31,GRAMD4,GSDMA,GSDMD,H2BC21,HLA-A,HLA-B,HLA-C,HLA-DPA1,HLA-DRB1,HLA-E,HLA-F,HLA-G,IDO1,IFI27,IFI35,IFI44L,IFIH1,IFIT2,IFIT3,IFIT5,IFITM1,IFITM2,IFITM3,IL12A,IL12RB1,IL12RB2,IL15,IL18BP,IL27,IL31RA,IL4I1,IRF1,IRF4,IRF7,ISG20,JAK2,JAK3,KLF4,KLRK1,LAG3,LILRA2,LITAF,LPL,LTA,LYN,MCOLN2,MEFV,MMP9,MSRB1,NCF1,NLRC5,NMI,NOD2,NUB1,OAS2,OAS3,OPTN,P2RX7,PARP14,PARP9,PDCD1,PDCD1LG2,PDE4B,PIM1,PLAAT3,PLSCR1,PLSCR4,PMAIP1,PML,PPM1E,PTGER4,PYHIN1,RAB20,RELB,RIPK2,RNF19B,RNF213,RSAD2,RTP4,SBNO2,SCIMP,SERINC5,SERPING1,SLAMF1,SLAMF6,SLAMF7,SLAMF8,SLC11A1,STAP1,STAT1,STAT2,STMN1,TANK,TAP2,TBX21,THBD,TICAM2,TIFA,TIFAB,TLR10,TLR5,TLR7,TLR8,TMEM255A,TNFRSF11A,TNFRSF14,TNFSF8,TRAFD1,TRDN,TRIM17,TRIM22,TRIM31,TRIM69,TSPAN32,TYRO3,UBD,UBE2L6,VCAM1,VWCE,ZBP1,ZC3H12A,ZNFX1
#> 8181 ACOD1,ADAM8,AIM2,APOBEC3A,APOBEC3D,APOBEC3G,APOL1,APPL2,AURKB,B2M,BANK1,BATF2,BATF3,C15orf48,C1QB,C1R,C1RL,C1S,C2,C3,C4A,C4B,CALCOCO2,CALHM6,CARD16,CASP4,CASP7,CCL13,CCL15,CCL18,CCL5,CCL7,CCL8,CD274,CD300H,CD300LF,CD40,CD74,CD80,CEACAM1,CFB,CFH,CIITA,CLEC10A,CLEC6A,CMPK2,COLEC12,CSF1,CSF2RB,CTSS,CX3CR1,CXADR,CXCL10,CXCL11,CXCL5,CXCL9,CYLD,CYP1A1,DDX60,DTX3L,E2F1,EDN1,FAM20A,FCN1,FGL2,GBP1,GBP2,GBP3,GBP4,GBP5,GBP6,GBP7,GCH1,GPR31,GRAMD4,GSDMA,GSDMD,H2BC21,HLA-A,HLA-B,HLA-C,HLA-DPA1,HLA-DRB1,HLA-E,HLA-F,HLA-G,IDO1,IFI27,IFI35,IFI44L,IFIH1,IFIT2,IFIT3,IFIT5,IFITM1,IFITM2,IFITM3,IL12A,IL12RB1,IL12RB2,IL15,IL18BP,IL27,IL31RA,IRF1,IRF4,IRF7,ISG20,JAK2,JAK3,KLRK1,LAG3,LILRA2,LITAF,LPL,LTA,LYN,MCOLN2,MEFV,MMP9,MSRB1,NCF1,NLRC5,NMI,NOD2,NUB1,OAS2,OAS3,OPTN,P2RX7,PARP14,PARP9,PDCD1LG2,PDE4B,PIM1,PLAAT3,PLSCR1,PLSCR4,PMAIP1,PML,PPM1E,PTGER4,PYHIN1,RAB20,RELB,RIPK2,RNF19B,RNF213,RSAD2,RTP4,SBNO2,SCIMP,SERINC5,SERPING1,SLAMF1,SLAMF6,SLAMF7,SLAMF8,SLC11A1,STAP1,STAT1,STAT2,STMN1,TANK,TAP2,TBX21,THBD,TICAM2,TIFA,TIFAB,TLR10,TLR5,TLR7,TLR8,TMEM255A,TNFRSF11A,TNFRSF14,TNFSF8,TRAFD1,TRDN,TRIM17,TRIM22,TRIM31,TRIM69,TSPAN32,TYRO3,UBD,UBE2L6,VCAM1,VWCE,ZBP1,ZC3H12A,ZNFX1
#> 6262 ACOD1,ADAM8,AIM2,APOBEC3A,APOBEC3D,APOBEC3G,APOL1,APPL2,AURKB,B2M,BANK1,BATF2,BATF3,C15orf48,C1QB,C1R,C1RL,C1S,C2,C3,C4A,C4B,CALCOCO2,CALHM6,CARD16,CASP4,CASP7,CCL13,CCL15,CCL18,CCL5,CCL7,CCL8,CD274,CD300H,CD300LF,CD40,CD74,CD80,CEACAM1,CFB,CFH,CIITA,CLEC10A,CLEC6A,CMPK2,COLEC12,CSF1,CSF2RB,CTSS,CX3CR1,CXADR,CXCL10,CXCL11,CXCL5,CXCL9,CYLD,CYP1A1,DDX60,DTX3L,E2F1,EDN1,FAM20A,FCN1,FGL2,GBP1,GBP2,GBP3,GBP4,GBP5,GBP6,GBP7,GCH1,GPR31,GRAMD4,GSDMA,GSDMD,H2BC21,HLA-A,HLA-B,HLA-C,HLA-DPA1,HLA-DRB1,HLA-E,HLA-F,HLA-G,IDO1,IFI27,IFI35,IFI44L,IFIH1,IFIT2,IFIT3,IFIT5,IFITM1,IFITM2,IFITM3,IL12A,IL12RB1,IL12RB2,IL15,IL18BP,IL27,IL31RA,IRF1,IRF4,IRF7,ISG20,JAK2,JAK3,KLRK1,LAG3,LILRA2,LITAF,LPL,LTA,LYN,MCOLN2,MEFV,MMP9,MSRB1,NCF1,NLRC5,NMI,NOD2,NUB1,OAS2,OAS3,OPTN,P2RX7,PARP14,PARP9,PDCD1LG2,PDE4B,PIM1,PLAAT3,PLSCR1,PLSCR4,PMAIP1,PML,PPM1E,PTGER4,PYHIN1,RAB20,RELB,RIPK2,RNF19B,RNF213,RSAD2,RTP4,SBNO2,SCIMP,SERINC5,SERPING1,SLAMF1,SLAMF6,SLAMF7,SLAMF8,SLC11A1,STAP1,STAT1,STAT2,STMN1,TANK,TAP2,TBX21,THBD,TICAM2,TIFA,TIFAB,TLR10,TLR5,TLR7,TLR8,TMEM255A,TNFRSF11A,TNFRSF14,TNFSF8,TRAFD1,TRDN,TRIM17,TRIM22,TRIM31,TRIM69,TSPAN32,TYRO3,UBD,UBE2L6,VCAM1,VWCE,ZBP1,ZC3H12A,ZNFX1The function will return a table with 10 columns
category: The computer readable GO term ID.over_represented_pvalue: p-value for the overrepresentation test for enrichment (as specified by thegoseqalgorithm)under_represented_pvalue: p-value for the underrepresentation test for enrichmentnumDEInCat: The number of DE genes associated with this term (as defined in theres_deor in thede_genesparameters) (similar to theAnnotatedcolumn of the output fromrun_topGO())numInCatThe overall number of detected genes associated with this term (as defined in thede_containeror in thebg_genesparameters).term: The human readable GO term name.ontology: The ontology used to run the enrichment tests (BP/MF/CC)p.adj: FDR of your findings adjusted for multiple testinggenes: Lists the DE gene identifiers associated with that term (separated by a comma)genesymbols: Lists the DE gene symbols associated with that term (separated by a comma)
mosdef and clusterProfiler
Parameters like top_de, min_counts, verbose, FDR_threshold and de_typecan also be used here (For more detail on these parameters see above). If you want to further customize the call of enrichGO() inside the function, have a look at the documentation for enrichGO() from clusterProfiler Those parameters can be added to the run_cluPro() function call within the ellipsis (...). For example, as we are doing in the chunk that follows, we set Biological Process as the ontology to be used, by specifying ont = "BP"
clupro_macrophage <- run_cluPro(
de_container = dds_macrophage,
res_de = res_macrophage_IFNg_vs_naive,
mapping = "org.Hs.eg.db",
keyType = "SYMBOL",
ont = "BP"
)
head(clupro_macrophage)Importantly, keyType is relevant for the enrichGO() function that is wrapped in this routine. If using DESeqDataset and DESeqResults, this has to be “SYMBOL” which is also the default. If you use vectors please specify here what type of IDs you provide.
Again, to save time when rendering the vignette, we load the objects provided alongside this package to demonstrate the output (see also this script included in the package to inspect the code used to generate the objects):
data(res_enrich_macrophage_cluPro, package = "mosdef")The function will return a large enrich result containing some metadata and the enrichment results with 9 columns.
head(res_enrich_macrophage_cluPro)
#> ID
#> GO:0002250 GO:0002250
#> GO:0002252 GO:0002252
#> GO:0009617 GO:0009617
#> GO:0002460 GO:0002460
#> GO:0019882 GO:0019882
#> GO:0002396 GO:0002396
#> Description
#> GO:0002250 adaptive immune response
#> GO:0002252 immune effector process
#> GO:0009617 response to bacterium
#> GO:0002460 adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
#> GO:0019882 antigen processing and presentation
#> GO:0002396 MHC protein complex assembly
#> GeneRatio BgRatio pvalue p.adjust qvalue
#> GO:0002250 99/789 374/13083 4.458881e-38 2.055544e-34 1.713618e-34
#> GO:0002252 90/789 488/13083 2.959548e-22 6.821758e-19 5.687005e-19
#> GO:0009617 86/789 485/13083 3.940453e-20 6.055163e-17 5.047928e-17
#> GO:0002460 60/789 261/13083 6.133599e-20 7.068973e-17 5.893098e-17
#> GO:0019882 36/789 103/13083 8.753721e-19 8.070930e-16 6.728386e-16
#> GO:0002396 16/789 18/13083 3.616983e-18 2.144588e-15 1.787850e-15
#> geneID
#> GO:0002250 IRF1/IL18BP/HLA-DPA1/HLA-DMA/TAP2/TAP1/HLA-DMB/ASCL2/CD40/C4A/CD74/HLA-DOA/P2RX7/CD274/HLA-DRA/IL12RB1/ITK/SLAMF7/C4B/PDCD1LG2/SERPING1/LAG3/LAMP3/HLA-DPB1/TBX21/ERAP2/C1QB/HLA-DRB1/NOD2/HLA-F/CEACAM1/HLA-DQB1/BTN3A2/HLA-DRB5/HLA-B/KLRK1/BTN3A1/HLA-E/TNFRSF11A/HLA-A/CTLA4/HLA-C/JAK2/CX3CR1/HLA-DQB2/CR1L/CD7/RIPK2/TLR8/BTN3A3/IL4I1/C2/TNFSF13B/SLC11A1/GPR183/IL27/CD28/MCOLN2/HLA-DOB/HLA-DQA1/ICAM1/CLEC6A/LILRB3/TNFSF18/CD80/PDCD1/CSF2RB/TNFRSF21/RNF19B/B2M/C3/SLAMF6/CLEC10A/ZC3H12A/CTSS/JAK3/FGL1/CD1A/EXO1/IRF7/RSAD2/LILRA1/C1S/C1RL/SIT1/SLAMF1/C1R/HLA-G/CD1C/RELB/BCL6/LYN/IL12A/UNG/LTA/TNFRSF14/PARP3/CTSL/IRF4
#> GO:0002252 TAP2/HLA-DMB/ASCL2/CD40/C4A/CD74/P2RX7/HLA-DRA/IL12RB1/SLAMF7/C4B/SERPING1/LAG3/TBX21/C1QB/HLA-DRB1/NOD2/HLA-F/CEACAM1/BTN3A2/HLA-B/CFH/KLRK1/CFB/HLA-E/HLA-A/NMI/HLA-C/SUCNR1/CX3CR1/FGL2/CR1L/RIPK2/TLR8/BTN3A3/IL4I1/C2/SLC11A1/GPR183/IL27/IFI35/CD28/ICAM1/TNFSF18/CD80/CSF2RB/RNF19B/B2M/C3/SLAMF6/SCIMP/S100A13/ZC3H12A/JAK3/PLPP4/STAP1/CD1A/EXO1/IRF7/RSAD2/C1S/C1RL/SLAMF1/NCF1/LILRA2/SBNO2/DDX60/DYSF/C1R/KARS1/HLA-G/SLAMF8/CD1C/PTGER4/RELB/BCL6/LITAF/LYN/IL12A/APPL2/DLL1/TLR7/FCN1/TICAM2/UNG/LTA/NR4A3/TNFRSF14/PARP3/IRF4
#> GO:0009617 GBP2/IL18BP/GBP5/GBP4/TAP2/IDO1/CD40/GBP1/P2RX7/CD274/GCH1/CXCL11/GBP3/C4B/PDCD1LG2/TRDN/PDE4B/CXCL10/HLA-DRB1/NOD2/HLA-B/KLRK1/NLRC5/CFB/HLA-E/ACOD1/BANK1/CXCL9/TNFRSF11A/HLA-A/OPTN/GBP7/JAK2/CX3CR1/THBD/COLEC12/RIPK2/PLAAT3/C2/SLC11A1/IL27/VCAM1/CYP1A1/H2BC21/CD80/GSDMD/FAM20A/CSF2RB/RNF213/B2M/C3/SCIMP/TLR10/ZC3H12A/GSDMA/CASP4/STAP1/ZNFX1/CARD16/CASP7/IL12RB2/GPR31/MMP9/EDN1/C15orf48/GBP6/LILRA2/SBNO2/SLAMF8/TMEM255A/PTGER4/PPM1E/CMPK2/LITAF/LYN/TNFSF8/IL12A/OAS2/CXCL5/TIFAB/TICAM2/LTA/LPL/TNFRSF14/OAS3/PLSCR4
#> GO:0002460 IL18BP/TAP2/ASCL2/CD40/C4A/CD74/P2RX7/CD274/HLA-DRA/IL12RB1/C4B/SERPING1/TBX21/C1QB/HLA-DRB1/NOD2/HLA-F/CEACAM1/BTN3A2/HLA-B/HLA-E/HLA-A/HLA-C/JAK2/CR1L/RIPK2/TLR8/BTN3A3/IL4I1/C2/TNFSF13B/SLC11A1/IL27/CD28/ICAM1/CLEC6A/CD80/CSF2RB/B2M/C3/SLAMF6/ZC3H12A/JAK3/CD1A/EXO1/IRF7/RSAD2/C1S/C1RL/SLAMF1/C1R/HLA-G/CD1C/RELB/BCL6/IL12A/UNG/LTA/PARP3/IRF4
#> GO:0019882 HLA-DPA1/HLA-DMA/TAP2/TAP1/HLA-DMB/CD74/HLA-DOA/HLA-DRA/HLA-DPB1/ERAP2/HLA-DRB1/NOD2/HLA-F/HLA-DQB1/HLA-DRB5/HLA-B/PSME1/HLA-E/HLA-A/HLA-C/FGL2/HLA-DQB2/SLC11A1/TAPBP/PSMB8/HLA-DOB/HLA-DQA1/ICAM1/B2M/CTSS/CD1A/TAPBPL/HLA-G/CD1C/RELB/CTSL
#> GO:0002396 HLA-DPA1/HLA-DMA/HLA-DMB/HLA-DOA/HLA-DRA/HLA-DPB1/HLA-DRB1/HLA-DQB1/HLA-DRB5/HLA-A/HLA-DQB2/TAPBP/HLA-DOB/HLA-DQA1/B2M/TAPBPL
#> Count
#> GO:0002250 99
#> GO:0002252 90
#> GO:0009617 86
#> GO:0002460 60
#> GO:0019882 36
#> GO:0002396 16The definitions of these columns are included in the extensive clusterProfiler package documentation, please refer to that for more details.
Alternative ways to run enrichment analyses, within mosdef
All of these functions tailored to run enrichment methods also work if you only have/provide a vector of differentially expressed genes and a vector of background genes. Most of the above mentioned parameters work here as well (top_de, verbose), however parameters like min_counts and de_type will not affect the result, since they need further information which can only be found in the DESeqDataset and DESeqResults (in this case, access to the counts from the DESeqDataset object de_container and the Log2FoldChange from the DESeqResults object passed to res_de).
res_subset <- deresult_to_df(res_macrophage_IFNg_vs_naive)[1:100, ]
myde <- res_subset$id
myassayed <- rownames(res_macrophage_IFNg_vs_naive)
## Here keys are Ensembl not symbols
res_enrich_macrophage_topGO_vec <- run_topGO(
de_genes = myde,
bg_genes = myassayed,
mapping = "org.Hs.eg.db",
gene_id = "ensembl"
)
#> Your dataset has 100 DE genes.
#> You selected 100 (100.00%) genes for the enrichment analysis.
#> 6075 GO terms were analyzed. Not all of them are significantly enriched.
#> We suggest further subsetting the output list by for example:
#> using a pvalue cutoff in the column:
#> 'p.value_elim'.
head(res_enrich_macrophage_topGO_vec)
#> GO.ID
#> 1 GO:0002503
#> 2 GO:0002250
#> 3 GO:0019886
#> 4 GO:0034341
#> 5 GO:0031640
#> 6 GO:0071346
#> Term
#> 1 peptide antigen assembly with MHC class II protein complex
#> 2 adaptive immune response
#> 3 antigen processing and presentation of exogenous peptide antigen via MHC class II
#> 4 response to type II interferon
#> 5 killing of cells of another organism
#> 6 cellular response to type II interferon
#> Annotated Significant Expected Rank in p.value_classic p.value_elim
#> 1 14 7 0.08 39 7.6e-13
#> 2 385 29 2.33 3 3.2e-12
#> 3 28 8 0.17 43 3.6e-12
#> 4 111 14 0.67 17 8.0e-10
#> 5 50 7 0.30 90 1.9e-08
#> 6 91 8 0.55 104 7.2e-08
#> p.value_classic
#> 1 7.6e-13
#> 2 1.3e-24
#> 3 3.6e-12
#> 4 3.6e-15
#> 5 1.9e-08
#> 6 7.2e-08
#> genes
#> 1 ENSG00000196126,ENSG00000204252,ENSG00000204257,ENSG00000204287,ENSG00000223865,ENSG00000231389,ENSG00000242574
#> 2 ENSG00000019582,ENSG00000026751,ENSG00000073861,ENSG00000078081,ENSG00000089041,ENSG00000089692,ENSG00000096996,ENSG00000101017,ENSG00000113263,ENSG00000120217,ENSG00000125347,ENSG00000137496,ENSG00000149131,ENSG00000164308,ENSG00000167207,ENSG00000168394,ENSG00000173369,ENSG00000183734,ENSG00000196126,ENSG00000197646,ENSG00000204252,ENSG00000204257,ENSG00000204267,ENSG00000204287,ENSG00000223865,ENSG00000224389,ENSG00000231389,ENSG00000242574,ENSG00000244731
#> 3 ENSG00000019582,ENSG00000196126,ENSG00000204252,ENSG00000204257,ENSG00000204287,ENSG00000223865,ENSG00000231389,ENSG00000242574
#> 4 ENSG00000019582,ENSG00000096996,ENSG00000101017,ENSG00000117226,ENSG00000117228,ENSG00000125347,ENSG00000131979,ENSG00000136436,ENSG00000154451,ENSG00000162645,ENSG00000162654,ENSG00000179583,ENSG00000213886,ENSG00000231389
#> 5 ENSG00000100342,ENSG00000117226,ENSG00000117228,ENSG00000154451,ENSG00000162645,ENSG00000169245,ENSG00000169248
#> 6 ENSG00000096996,ENSG00000117226,ENSG00000117228,ENSG00000125347,ENSG00000154451,ENSG00000162645,ENSG00000162654,ENSG00000231389