Why doesn't the GOsummaries function work with my gene lists? INTERNAL SERVER ERROR
I need to compare two sets of genes with the GOsummaries library. I have obtained the two gene lists with the R function "enrichGO". In the user guide of the GOsummaries library it says the following to create a gosummaries object:
"The gosummaries function requires a set of gene lists as an input. It applies GO enrichment analysis to these gene lists using g:Profiler (http://biit.cs.ut.ee/gprofiler/) web toolkit and saves the results into a gosummaries object. Then one can add experimental data and configure the slots for additional information."
Inside g:Profiler (http://biit.cs.ut.ee/gprofiler/) I have tested my two gene lists and I get one result for each, so, I don't know, but I don't think it's the fault of that.
I show the two gene lists:
trad_genes$SYMBOL
[1] "AKAP7" "ARHGAP5" "ATXN7" "BAZ2A" "CHD6" "CNTLN" "DDX3Y"
[8] "ELK4" "ERICH1" "ERICH1" "FKBP8" "GSE1" "HOMER1" "LINC01004"
[15] "NCAPG" "NUB1" "PDHX" "POLD1" "RAB3D" "RAD54L2" "SAFB"
[22] "SH2B3" "SLC38A1" "SLC39A8" "TXLNGY" "UTY" "ZFY"
genes_pvalue_EA$SYMBOL
[1] "AAGAB" "AKAP10" "AKAP8L" "AKR1A1" "ANAPC1" "ANKRD26" "ANKRD27"
[8] "ANP32B" "AP3B1" "APOOL" "APPL1" "ARHGAP42" "ATAD2" "ATAD5"
[15] "ATF7IP2" "ATG4C" "ATL2" "ATRIP" "ATXN3" "B4GALT5" "BAZ1B"
[22] "BBS9" "BCLAF3" "BUD23" "C5" "CA13" "CAMTA1" "CAPRIN2"
[29] "CBR4" "CCDC88A" "CCDC88C" "CENPH" "CENPI" "CHD2" "COG3"
[36] "CPSF2" "CSTF3" "CUL1" "CUL2" "CUL3" "DCAF7" "DDX21"
[43] "DDX60" "DHDDS" "DIPK2A" "DMTN" "DNAJC2" "EHBP1" "ELF2"
[50] "ELK4" "ERMARD" "ERMARD" "ESPL1" "FAM168B" "FAM193A" "FAM216A"
[57] "FANCM" "FBXO33" "FBXW7" "FKBP3" "FOXJ3" "FRMD4A" "FUNDC1"
[64] "GIMAP8" "GLS" "GLYR1" "GRHPR" "GTF2IP1" "GTPBP10" "HECTD2"
[71] "HIP1" "IKZF1" "ITGB3BP" "KATNAL1" "KDM3B" "KDM4C" "KHDC4"
[78] "KHDRBS1" "KIAA2026" "KIF24" "LDLRAD4" "LINC00910" "MAP3K5" "MAP4K5"
[85] "MAPK9" "MARCHF3" "METTL25" "MLH3" "MMS19" "MYCBP2" "MYO19"
[92] "MYO19" "MYO9A" "MYSM1" "NAA15" "NBAS" "NBEAL1" "NCAPD3"
[99] "NCEH1" "NCOR2" "NEDD4L" "NEK9" "NEMF" "NIPBL" "NMRAL1"
[106] "NMRAL1" "NMRK1" "NPEPPS" "NPLOC4" "NSD2" "NSUN6" "NUP43"
[113] "NUP88" "OTUD7B" "PACRGL" "PAM" "PAXBP1" "PAXBP1" "PCCA"
[120] "PCGF6" "PDPK2P" "PGS1" "PHACTR4" "PIAS1" "PIP4K2B" "PIP4K2B"
[127] "POLB" "PRKCSH" "PTK2" "PTPN7" "PUS7" "RAB21" "RAB27A"
[134] "RABGAP1L" "RAD51C" "RALGAPA1" "RALGAPB" "RASGRP3" "RBBP8" "RBL1"
[141] "RBM41" "REV3L" "RNPS1" "RTN4" "SAP130" "SCAF8" "SCARF1"
[148] "SCARF1" "SCLT1" "SGO1" "SIAE" "SIRT1" "SKA3" "SLAIN1"
[155] "SLC15A4" "SLC37A3" "SLC39A11" "SLC39A11" "SLC6A9" "SLCO4C1" "SMARCD1"
[162] "SOS2" "SPG11" "SPG7" "SUPT20H" "SUZ12P1" "SYPL1" "TARS2"
[169] "TBX21" "TIAL1" "TMCC2" "TMEM209" "TMEM41B" "TNFRSF21" "TNPO2"
[176] "TOGARAM1" "TPRA1" "TRA2B" "TRAPPC9" "TRIM33" "TSC22D1" "TTPAL"
[183] "TUT7" "TXLNG" "U2AF1" "UBE2G1" "UBR3" "USP31" "USP6NL"
[190] "UTRN" "VPS13A" "WDPCP" "WIPI1" "WIPI2" "WWC3" "XPO1"
[197] "YME1L1" "ZBTB16" "ZBTB8OS" "ZC3H14" "ZCCHC7" "ZFX" "ZFYVE1"
[204] "ZNF451"
And the code I have tried to reproduce with them is as follows:
genes1 = trad_genes$SYMBOL
genes2 = genes_pvalue_EA$SYMBOL
gl = list(List = list(genes1, genes2))
gs = gosummaries(gl)
Warning: Please consider using the new package "gprofiler2". At the moment you are using a deprecated package relying on outdated data.
More information at https://biit.cs.ut.ee/gprofiler/page/r-new. Feel free to contact us at biit.support@ut.ee for further help.
Error: INTERNAL SERVER ERROR
But all I get is a warning and an error. The warning tells me to use "gprofiler2". But I tried to uninstall the "gprofiler" library and use only "gprofiler2" and the "GOsummaries" library doesn't work because it needs the "gprofiler" library. As for the INTERNAL SERVER ERROR, I don't know what to do.
I'm new asking on stackoverflow, but if some more information is needed to solve this I'm willing to give anything.
Many thanks in advance.
Solution
Are you looking for this?
> gostres_trad_genes <- gprofiler2::gost(trad_genes)
> gostres_trad_genes$result
query significant p_value term_size query_size intersection_size
1 query_1 TRUE 0.03019194 288 23 5
2 query_1 TRUE 0.02249582 257 24 5
precision recall term_id source
1 0.2173913 0.01736111 MIRNA:hsa-miR-181d-5p MIRNA
2 0.2083333 0.01945525 TF:M01882 TF
term_name effective_domain_size source_order
1 hsa-miR-181d-5p 14846 315
2 Factor: IRF-2; motif: NNRAAAGTGAAASNNA 20011 4282
parents
1 MIRNA:000000
2 TF:M00000
> gostres_genes_pvalue_EAs <- gprofiler2::gost(genes_pvalue_EA)
> gostres_genes_pvalue_EAs$result |> head()
query significant p_value term_size query_size intersection_size
1 query_1 TRUE 2.825648e-06 1276 184 35
2 query_1 TRUE 3.576819e-05 1273 184 33
3 query_1 TRUE 2.517966e-04 191 184 12
4 query_1 TRUE 6.533390e-04 1811 184 38
5 query_1 TRUE 7.115125e-04 3562 184 59
6 query_1 TRUE 1.906513e-03 1019 184 26
precision recall term_id source
1 0.19021739 0.02742947 GO:0043687 GO:BP
2 0.17934783 0.02592302 GO:0022402 GO:BP
3 0.06521739 0.06282723 GO:1901875 GO:BP
4 0.20652174 0.02098288 GO:0007049 GO:BP
5 0.32065217 0.01656373 GO:0006996 GO:BP
6 0.14130435 0.02551521 GO:0070647 GO:BP
term_name
1 post-translational protein modification
2 cell cycle process
3 positive regulation of post-translational protein modification
4 cell cycle
5 organelle organization
6 protein modification by small protein conjugation or removal
effective_domain_size source_order parents
1 21010 11358 GO:0036211
2 21010 6908 GO:0007049, GO:0009987
3 21010 22698 GO:0031401, GO:0043687, GO:1901873
4 21010 2692 GO:0009987
5 21010 2654 GO:0016043
6 21010 17034 GO:0043687
> gprofiler2::gostplot(gostres_genes_pvalue_EAs)
Data:
> dput(trad_genes)
c("AKAP7", "ARHGAP5", "ATXN7", "BAZ2A", "CHD6", "CNTLN", "DDX3Y",
"ELK4", "ERICH1", "ERICH1", "FKBP8", "GSE1", "HOMER1", "LINC01004",
"NCAPG", "NUB1", "PDHX", "POLD1", "RAB3D", "RAD54L2", "SAFB",
"SH2B3", "SLC38A1", "SLC39A8", "TXLNGY", "UTY", "ZFY")
> dput(genes_pvalue_EA)
c("AAGAB", "AKAP10", "AKAP8L", "AKR1A1", "ANAPC1", "ANKRD26",
"ANKRD27", "ANP32B", "AP3B1", "APOOL", "APPL1", "ARHGAP42", "ATAD2",
"ATAD5", "ATF7IP2", "ATG4C", "ATL2", "ATRIP", "ATXN3", "B4GALT5",
"BAZ1B", "BBS9", "BCLAF3", "BUD23", "C5", "CA13", "CAMTA1", "CAPRIN2",
"CBR4", "CCDC88A", "CCDC88C", "CENPH", "CENPI", "CHD2", "COG3",
"CPSF2", "CSTF3", "CUL1", "CUL2", "CUL3", "DCAF7", "DDX21", "DDX60",
"DHDDS", "DIPK2A", "DMTN", "DNAJC2", "EHBP1", "ELF2", "ELK4",
"ERMARD", "ERMARD", "ESPL1", "FAM168B", "FAM193A", "FAM216A",
"FANCM", "FBXO33", "FBXW7", "FKBP3", "FOXJ3", "FRMD4A", "FUNDC1",
"GIMAP8", "GLS", "GLYR1", "GRHPR", "GTF2IP1", "GTPBP10", "HECTD2",
"HIP1", "IKZF1", "ITGB3BP", "KATNAL1", "KDM3B", "KDM4C", "KHDC4",
"KHDRBS1", "KIAA2026", "KIF24", "LDLRAD4", "LINC00910", "MAP3K5",
"MAP4K5", "MAPK9", "MARCHF3", "METTL25", "MLH3", "MMS19", "MYCBP2",
"MYO19", "MYO19", "MYO9A", "MYSM1", "NAA15", "NBAS", "NBEAL1",
"NCAPD3", "NCEH1", "NCOR2", "NEDD4L", "NEK9", "NEMF", "NIPBL",
"NMRAL1", "NMRAL1", "NMRK1", "NPEPPS", "NPLOC4", "NSD2", "NSUN6",
"NUP43", "NUP88", "OTUD7B", "PACRGL", "PAM", "PAXBP1", "PAXBP1",
"PCCA", "PCGF6", "PDPK2P", "PGS1", "PHACTR4", "PIAS1", "PIP4K2B",
"PIP4K2B", "POLB", "PRKCSH", "PTK2", "PTPN7", "PUS7", "RAB21",
"RAB27A", "RABGAP1L", "RAD51C", "RALGAPA1", "RALGAPB", "RASGRP3",
"RBBP8", "RBL1", "RBM41", "REV3L", "RNPS1", "RTN4", "SAP130",
"SCAF8", "SCARF1", "SCARF1", "SCLT1", "SGO1", "SIAE", "SIRT1",
"SKA3", "SLAIN1", "SLC15A4", "SLC37A3", "SLC39A11", "SLC39A11",
"SLC6A9", "SLCO4C1", "SMARCD1", "SOS2", "SPG11", "SPG7", "SUPT20H",
"SUZ12P1", "SYPL1", "TARS2", "TBX21", "TIAL1", "TMCC2", "TMEM209",
"TMEM41B", "TNFRSF21", "TNPO2", "TOGARAM1", "TPRA1", "TRA2B",
"TRAPPC9", "TRIM33", "TSC22D1", "TTPAL", "TUT7", "TXLNG", "U2AF1",
"UBE2G1", "UBR3", "USP31", "USP6NL", "UTRN", "VPS13A", "WDPCP",
"WIPI1", "WIPI2", "WWC3", "XPO1", "YME1L1", "ZBTB16", "ZBTB8OS",
"ZC3H14", "ZCCHC7", "ZFX", "ZFYVE1", "ZNF451")
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