Extract functional terms enriched in the DE genes, based on goseq
Source:R/run_enrichment.R
run_goseq.RdA wrapper for extracting functional GO terms enriched in a list of (DE) genes, based on the algorithm and the implementation in the goseq package
Usage
run_goseq(
de_container = NULL,
res_de = NULL,
de_genes = NULL,
bg_genes = NULL,
top_de = NULL,
FDR_threshold = 0.05,
min_counts = 0,
genome = "hg38",
id = "ensGene",
de_type = "up_and_down",
testCats = c("GO:BP", "GO:MF", "GO:CC"),
mapping = "org.Hs.eg.db",
add_gene_to_terms = TRUE,
verbose = TRUE
)Arguments
- de_container
An object containing the data for a Differential Expression workflow (e.g.
DESeq2,edgeRorlimma). Currently, this can be aDESeqDataSetobject, normally obtained after running your data through theDESeq2framework.- res_de
An object containing the results of the Differential Expression analysis workflow (e.g.
DESeq2,edgeRorlimma). Currently, this can be aDESeqResultsobject created using theDESeq2framework.- de_genes
A vector of (differentially expressed) genes
- bg_genes
A vector of background genes, e.g. all (expressed) genes in the assays
- top_de
numeric, how many of the top differentially expressed genes to use for the enrichment analysis. Attempts to reduce redundancy. Assumes the data is sorted by padj (default in DESeq2).
- FDR_threshold
The pvalue threshold to us for counting genes as de. Default is 0.05
- min_counts
numeric, min number of counts a gene needs to have to be included in the geneset that the de genes are compared to. Default is 0, recommended only for advanced users.
- genome
A string identifying the genome that genes refer to, as in the
goseq::goseq()function- id
A string identifying the gene identifier used by genes, as in the
goseq::goseq()function- de_type
One of: 'up', 'down', or 'up_and_down' Which genes to use for GOterm calculations: upregulated, downregulated or both
- testCats
A vector specifying which categories to test for overrepresentation amongst DE genes - can be any combination of "GO:CC", "GO:BP", "GO:MF" & "KEGG"
- mapping
Character string, named as the
org.XX.eg.dbpackage which should be available in Bioconductor- add_gene_to_terms
Logical, whether to add a column with all genes annotated to each GO term
- verbose
Logical, whether to add messages telling the user which steps were taken
Details
Note: the feature length retrieval is based on the goseq::goseq()
function, and requires that the corresponding TxDb packages are installed
and available
See also
goseq::goseq() for the underlying method
Other Enrichment functions:
run_cluPro(),
run_topGO()
Examples
library("macrophage")
library("DESeq2")
data(gse, package = "macrophage")
dds_macrophage <- DESeqDataSet(gse, design = ~ line + condition)
#> using counts and average transcript lengths from tximeta
rownames(dds_macrophage) <- substr(rownames(dds_macrophage), 1, 15)
keep <- rowSums(counts(dds_macrophage) >= 10) >= 6
dds_macrophage <- dds_macrophage[keep, ]
dds_macrophage <- DESeq(dds_macrophage)
#> estimating size factors
#> using 'avgTxLength' from assays(dds), correcting for library size
#> estimating dispersions
#> gene-wise dispersion estimates
#> mean-dispersion relationship
#> final dispersion estimates
#> fitting model and testing
data(res_de_macrophage, package = "mosdef")
res_de <- res_macrophage_IFNg_vs_naive
mygo <- run_goseq(
res_de = res_macrophage_IFNg_vs_naive,
de_container = dds_macrophage,
mapping = "org.Hs.eg.db",
testCats = "GO:BP",
add_gene_to_terms = TRUE
)
#> 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: 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
#> Warning: 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(mygo)
#> 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,ZNFX1