# source('http://bioconductor.org/biocLite.R') biocLite('biomaRt')
library("biomaRt")
listMarts()
## biomart
## 1 ensembl
## 2 snp
## 3 functional_genomics
## 4 vega
## 5 fungi_mart_21
## 6 fungi_variations_21
## 7 metazoa_mart_21
## 8 metazoa_variations_21
## 9 plants_mart_21
## 10 plants_variations_21
## 11 protists_mart_21
## 12 protists_variations_21
## 13 msd
## 14 htgt
## 15 REACTOME
## 16 WS220
## 17 biomart
## 18 pride
## 19 prod-intermart_1
## 20 unimart
## 21 biomartDB
## 22 biblioDB
## 23 Eurexpress Biomart
## 24 phytozome_mart
## 25 HapMap_rel27
## 26 CosmicMart
## 27 cildb_all_v2
## 28 cildb_inp_v2
## 29 experiments
## 30 combinations
## 31 oncomodules
## 32 gmap_japonica
## 33 europhenomeannotations
## 34 ikmc
## 35 EMAGE gene expression
## 36 EMAP anatomy ontology
## 37 EMAGE browse repository
## 38 GermOnline
## 39 Sigenae_Oligo_Annotation_Ensembl_61
## 40 Sigenae Oligo Annotation (Ensembl 59)
## 41 Sigenae Oligo Annotation (Ensembl 56)
## 42 K562_Gm12878
## 43 Hsmm_Hmec
## 44 Pancreas63
## 45 Public_OBIOMART
## 46 Public_VITIS
## 47 Public_VITIS_12x
## 48 Prod_WHEAT
## 49 Public_TAIRV10
## 50 Public_MAIZE
## 51 Prod_POPLAR
## 52 Prod_POPLAR_V2
## 53 Prod_BOTRYTISEDIT
## 54 Prod_
## 55 Prod_SCLEROEDIT
## 56 Prod_LMACULANSEDIT
## 57 vb_mart_22
## 58 vb_snp_mart_22
## 59 expression
## 60 ENSEMBL_MART_PLANT
## 61 ENSEMBL_MART_PLANT_SNP
## version
## 1 ENSEMBL GENES 75 (SANGER UK)
## 2 ENSEMBL VARIATION 75 (SANGER UK)
## 3 ENSEMBL REGULATION 75 (SANGER UK)
## 4 VEGA 53 (SANGER UK)
## 5 ENSEMBL FUNGI 21 (EBI UK)
## 6 ENSEMBL FUNGI VARIATION 21 (EBI UK)
## 7 ENSEMBL METAZOA 21 (EBI UK)
## 8 ENSEMBL METAZOA VARIATION 21 (EBI UK)
## 9 ENSEMBL PLANTS 21 (EBI UK)
## 10 ENSEMBL PLANTS VARIATION 21 (EBI UK)
## 11 ENSEMBL PROTISTS 21 (EBI UK)
## 12 ENSEMBL PROTISTS VARIATION 21 (EBI UK)
## 13 MSD (EBI UK)
## 14 WTSI MOUSE GENETICS PROJECT (SANGER UK)
## 15 REACTOME (CSHL US)
## 16 WORMBASE 220 (CSHL US)
## 17 MGI (JACKSON LABORATORY US)
## 18 PRIDE (EBI UK)
## 19 INTERPRO (EBI UK)
## 20 UNIPROT (EBI UK)
## 21 PARAMECIUM GENOME (CNRS FRANCE)
## 22 PARAMECIUM BIBLIOGRAPHY (CNRS FRANCE)
## 23 EUREXPRESS (MRC EDINBURGH UK)
## 24 PHYTOZOME (JGI/CIG US)
## 25 HAPMAP 27 (NCBI US)
## 26 COSMIC (SANGER UK)
## 27 CILDB INPARANOID AND FILTERED BEST HIT (CNRS FRANCE)
## 28 CILDB INPARANOID (CNRS FRANCE)
## 29 INTOGEN EXPERIMENTS
## 30 INTOGEN COMBINATIONS
## 31 INTOGEN ONCOMODULES
## 32 RICE-MAP JAPONICA (PEKING UNIVESITY CHINA)
## 33 EUROPHENOME
## 34 IKMC GENES AND PRODUCTS (IKMC)
## 35 EMAGE GENE EXPRESSION
## 36 EMAP ANATOMY ONTOLOGY
## 37 EMAGE BROWSE REPOSITORY
## 38 GERMONLINE
## 39 SIGENAE OLIGO ANNOTATION (ENSEMBL 61)
## 40 SIGENAE OLIGO ANNOTATION (ENSEMBL 59)
## 41 SIGENAE OLIGO ANNOTATION (ENSEMBL 56)
## 42 Predictive models of gene regulation from processed high-throughput epigenomics data: K562 vs. Gm12878
## 43 Predictive models of gene regulation from processed high-throughput epigenomics data: Hsmm vs. Hmec
## 44 PANCREATIC EXPRESSION DATABASE (BARTS CANCER INSTITUTE UK)
## 45 Genetic maps (markers, Qtls), Polymorphisms (snps, genes), Genetic and Phenotype resources with Genes annotations
## 46 Grapevine 8x, stuctural annotation with Genetic maps (genetic markers..)
## 47 Grapevine 12x, stuctural and functional annotation with Genetic maps (genetic markers..)
## 48 Wheat, stuctural annotation with Genetic maps (genetic markers..) and Polymorphisms (snps)
## 49 Arabidopsis Thaliana TAIRV10, genes functional annotation
## 50 Zea mays ZmB73, genes functional annotation
## 51 Populus trichocarpa, genes functional annotation
## 52 Populus trichocarpa, genes functional annotation V2.0
## 53 Botrytis cinerea T4, genes functional annotation
## 54 Botrytis cinerea B0510, genes functional annotation
## 55 Sclerotinia sclerotiorum, genes functional annotation
## 56 Leptosphaeria maculans, genes functional annotation
## 57 VectorBase Genes
## 58 VectorBase Variation
## 59 VectorBase Expression
## 60 GRAMENE 40 ENSEMBL GENES (CSHL/CORNELL US)
## 61 GRAMENE 40 VARIATION (CSHL/CORNELL US)
ensembl = useMart("ensembl")
listDatasets(ensembl)
## dataset
## 1 oanatinus_gene_ensembl
## 2 cporcellus_gene_ensembl
## 3 gaculeatus_gene_ensembl
## 4 lafricana_gene_ensembl
## 5 itridecemlineatus_gene_ensembl
## 6 choffmanni_gene_ensembl
## 7 csavignyi_gene_ensembl
## 8 fcatus_gene_ensembl
## 9 rnorvegicus_gene_ensembl
## 10 psinensis_gene_ensembl
## 11 cjacchus_gene_ensembl
## 12 ttruncatus_gene_ensembl
## 13 scerevisiae_gene_ensembl
## 14 celegans_gene_ensembl
## 15 oniloticus_gene_ensembl
## 16 trubripes_gene_ensembl
## 17 amexicanus_gene_ensembl
## 18 pmarinus_gene_ensembl
## 19 eeuropaeus_gene_ensembl
## 20 falbicollis_gene_ensembl
## 21 ptroglodytes_gene_ensembl
## 22 etelfairi_gene_ensembl
## 23 cintestinalis_gene_ensembl
## 24 nleucogenys_gene_ensembl
## 25 sscrofa_gene_ensembl
## 26 ocuniculus_gene_ensembl
## 27 dnovemcinctus_gene_ensembl
## 28 pcapensis_gene_ensembl
## 29 tguttata_gene_ensembl
## 30 mlucifugus_gene_ensembl
## 31 hsapiens_gene_ensembl
## 32 mfuro_gene_ensembl
## 33 tbelangeri_gene_ensembl
## 34 ggallus_gene_ensembl
## 35 xtropicalis_gene_ensembl
## 36 ecaballus_gene_ensembl
## 37 pabelii_gene_ensembl
## 38 xmaculatus_gene_ensembl
## 39 drerio_gene_ensembl
## 40 lchalumnae_gene_ensembl
## 41 tnigroviridis_gene_ensembl
## 42 amelanoleuca_gene_ensembl
## 43 mmulatta_gene_ensembl
## 44 pvampyrus_gene_ensembl
## 45 mdomestica_gene_ensembl
## 46 acarolinensis_gene_ensembl
## 47 vpacos_gene_ensembl
## 48 tsyrichta_gene_ensembl
## 49 ogarnettii_gene_ensembl
## 50 dmelanogaster_gene_ensembl
## 51 mmurinus_gene_ensembl
## 52 loculatus_gene_ensembl
## 53 olatipes_gene_ensembl
## 54 ggorilla_gene_ensembl
## 55 oprinceps_gene_ensembl
## 56 dordii_gene_ensembl
## 57 oaries_gene_ensembl
## 58 mmusculus_gene_ensembl
## 59 mgallopavo_gene_ensembl
## 60 gmorhua_gene_ensembl
## 61 aplatyrhynchos_gene_ensembl
## 62 saraneus_gene_ensembl
## 63 sharrisii_gene_ensembl
## 64 meugenii_gene_ensembl
## 65 btaurus_gene_ensembl
## 66 cfamiliaris_gene_ensembl
## description version
## 1 Ornithorhynchus anatinus genes (OANA5) OANA5
## 2 Cavia porcellus genes (cavPor3) cavPor3
## 3 Gasterosteus aculeatus genes (BROADS1) BROADS1
## 4 Loxodonta africana genes (loxAfr3) loxAfr3
## 5 Ictidomys tridecemlineatus genes (spetri2) spetri2
## 6 Choloepus hoffmanni genes (choHof1) choHof1
## 7 Ciona savignyi genes (CSAV2.0) CSAV2.0
## 8 Felis catus genes (Felis_catus_6.2) Felis_catus_6.2
## 9 Rattus norvegicus genes (Rnor_5.0) Rnor_5.0
## 10 Pelodiscus sinensis genes (PelSin_1.0) PelSin_1.0
## 11 Callithrix jacchus genes (C_jacchus3.2.1) C_jacchus3.2.1
## 12 Tursiops truncatus genes (turTru1) turTru1
## 13 Saccharomyces cerevisiae genes (R64-1-1) R64-1-1
## 14 Caenorhabditis elegans genes (WBcel235) WBcel235
## 15 Oreochromis niloticus genes (Orenil1.0) Orenil1.0
## 16 Takifugu rubripes genes (FUGU4.0) FUGU4.0
## 17 Astyanax mexicanus genes (AstMex102) AstMex102
## 18 Petromyzon marinus genes (Pmarinus_7.0) Pmarinus_7.0
## 19 Erinaceus europaeus genes (eriEur1) eriEur1
## 20 Ficedula albicollis genes (FicAlb_1.4) FicAlb_1.4
## 21 Pan troglodytes genes (CHIMP2.1.4) CHIMP2.1.4
## 22 Echinops telfairi genes (TENREC) TENREC
## 23 Ciona intestinalis genes (KH) KH
## 24 Nomascus leucogenys genes (Nleu1.0) Nleu1.0
## 25 Sus scrofa genes (Sscrofa10.2) Sscrofa10.2
## 26 Oryctolagus cuniculus genes (OryCun2.0) OryCun2.0
## 27 Dasypus novemcinctus genes (Dasnov3.0) Dasnov3.0
## 28 Procavia capensis genes (proCap1) proCap1
## 29 Taeniopygia guttata genes (taeGut3.2.4) taeGut3.2.4
## 30 Myotis lucifugus genes (myoLuc2) myoLuc2
## 31 Homo sapiens genes (GRCh37.p13) GRCh37.p13
## 32 Mustela putorius furo genes (MusPutFur1.0) MusPutFur1.0
## 33 Tupaia belangeri genes (tupBel1) tupBel1
## 34 Gallus gallus genes (Galgal4) Galgal4
## 35 Xenopus tropicalis genes (JGI4.2) JGI4.2
## 36 Equus caballus genes (EquCab2) EquCab2
## 37 Pongo abelii genes (PPYG2) PPYG2
## 38 Xiphophorus maculatus genes (Xipmac4.4.2) Xipmac4.4.2
## 39 Danio rerio genes (Zv9) Zv9
## 40 Latimeria chalumnae genes (LatCha1) LatCha1
## 41 Tetraodon nigroviridis genes (TETRAODON8.0) TETRAODON8.0
## 42 Ailuropoda melanoleuca genes (ailMel1) ailMel1
## 43 Macaca mulatta genes (MMUL_1) MMUL_1
## 44 Pteropus vampyrus genes (pteVam1) pteVam1
## 45 Monodelphis domestica genes (monDom5) monDom5
## 46 Anolis carolinensis genes (AnoCar2.0) AnoCar2.0
## 47 Vicugna pacos genes (vicPac1) vicPac1
## 48 Tarsius syrichta genes (tarSyr1) tarSyr1
## 49 Otolemur garnettii genes (OtoGar3) OtoGar3
## 50 Drosophila melanogaster genes (BDGP5) BDGP5
## 51 Microcebus murinus genes (micMur1) micMur1
## 52 Lepisosteus oculatus genes (LepOcu1) LepOcu1
## 53 Oryzias latipes genes (HdrR) HdrR
## 54 Gorilla gorilla genes (gorGor3.1) gorGor3.1
## 55 Ochotona princeps genes (OchPri2.0) OchPri2.0
## 56 Dipodomys ordii genes (dipOrd1) dipOrd1
## 57 Ovis aries genes (Oar_v3.1) Oar_v3.1
## 58 Mus musculus genes (GRCm38.p2) GRCm38.p2
## 59 Meleagris gallopavo genes (UMD2) UMD2
## 60 Gadus morhua genes (gadMor1) gadMor1
## 61 Anas platyrhynchos genes (BGI_duck_1.0) BGI_duck_1.0
## 62 Sorex araneus genes (sorAra1) sorAra1
## 63 Sarcophilus harrisii genes (DEVIL7.0) DEVIL7.0
## 64 Macropus eugenii genes (Meug_1.0) Meug_1.0
## 65 Bos taurus genes (UMD3.1) UMD3.1
## 66 Canis familiaris genes (CanFam3.1) CanFam3.1
ensembl = useDataset("hsapiens_gene_ensembl", mart = ensembl)
filters = listFilters(ensembl)
attributes = listAttributes(ensembl)
affyids = c("202763_at", "209310_s_at", "207500_at")
entrezID <- getBM(attributes = c("affy_hg_u133_plus_2", "entrezgene"), filters = "affy_hg_u133_plus_2",
values = affyids, mart = ensembl)
Bei which immer zuerst wo man sucht
which(attributes$name %in% c("affy_hg_u133_plus_2", "entrezgene"))
## [1] 50 94
getBM(attributes = c("hgnc_id", "chromosome_name"), filters = "affy_hg_u133_plus_2",
values = affyids, mart = ensembl)
## hgnc_id chromosome_name
## 1 1505 11
## 2 1506 11
## 3 1504 4
entrzSearch <- entrezID$entrezgene
at <- listAttributes(ensembl)
at[grep("^go", at$name), ]
## name description
## 28 go_id GO Term Accession
## 31 go_linkage_type GO Term Evidence Code
## 33 goslim_goa_accession GOSlim GOA Accession(s)
## 34 goslim_goa_description GOSlim GOA Description
result <- getBM(attributes = c("go_id"), filters = "entrezgene", values = entrzSearch,
mart = ensembl)
goSearch <- c("GO:0051330", "GO:0000080", "GO:0000114", "GO:0000082")
chrom <- c(1, 2, "Y")
result3 <- getBM(attributes = "hgnc_symbol", filters = c("go_id", "chromosome_name"),
values = list(goSearch, chrom), mart = ensembl)
refseqids = c("NM_005359", "NM_000546")
result4 <- getBM(attributes = c("refseq_mrna", "interpro", "interpro_description"),
filters = c("refseq_mrna"), values = list(refseqids), mart = ensembl)
print(result4)
## refseq_mrna interpro interpro_description
## 1 NM_000546 IPR002117 p53 tumour suppressor family
## 2 NM_000546 IPR011615 p53, DNA-binding domain
## 3 NM_000546 IPR010991 p53, tetramerisation domain
## 4 NM_000546 IPR013872 p53 transactivation domain
## 5 NM_000546 IPR008967 p53-like transcription factor, DNA-binding
## 6 NM_005359 IPR001132 SMAD domain, Dwarfin-type
## 7 NM_005359 IPR003619 MAD homology 1, Dwarfin-type
## 8 NM_005359 IPR013019 MAD homology, MH1
## 9 NM_005359 IPR008984 SMAD/FHA domain
start <- 1100000
stop <- 1250000
chr <- 16
sort(filters$name)
## [1] "affy_hc_g110"
## [2] "affy_hg_focus"
## [3] "affy_hg_u133_plus_2"
## [4] "affy_hg_u133a"
## [5] "affy_hg_u133a_2"
## [6] "affy_hg_u133b"
## [7] "affy_hg_u95a"
## [8] "affy_hg_u95av2"
## [9] "affy_hg_u95b"
## [10] "affy_hg_u95c"
## [11] "affy_hg_u95d"
## [12] "affy_hg_u95e"
## [13] "affy_huex_1_0_st_v2"
## [14] "affy_hugene_1_0_st_v1"
## [15] "affy_hugene_2_0_st_v1"
## [16] "affy_hugenefl"
## [17] "affy_primeview"
## [18] "affy_u133_x3p"
## [19] "agilent_cgh_44b"
## [20] "anatomical_system_term"
## [21] "arrayexpress"
## [22] "atlas_celltype"
## [23] "atlas_diseasestate"
## [24] "atlas_organismpart"
## [25] "band_end"
## [26] "band_start"
## [27] "biotype"
## [28] "ccds"
## [29] "cell_type_term"
## [30] "chembl"
## [31] "chromosomal_region"
## [32] "chromosome_name"
## [33] "clone_based_ensembl_gene_name"
## [34] "clone_based_ensembl_transcript_name"
## [35] "clone_based_vega_gene_name"
## [36] "clone_based_vega_transcript_name"
## [37] "codelink"
## [38] "dbass3_name"
## [39] "development_stage_term"
## [40] "efg_agilent_sureprint_g3_ge_8x60k"
## [41] "efg_agilent_sureprint_g3_ge_8x60k_v2"
## [42] "efg_agilent_wholegenome_4x44k_v1"
## [43] "efg_agilent_wholegenome_4x44k_v2"
## [44] "embl"
## [45] "encode_region"
## [46] "end"
## [47] "ens_hs_gene"
## [48] "ens_hs_transcript"
## [49] "ens_hs_translation"
## [50] "ens_lrg_gene"
## [51] "ens_lrg_transcript"
## [52] "ensembl_exon_id"
## [53] "ensembl_gene_id"
## [54] "ensembl_peptide_id"
## [55] "ensembl_transcript_id"
## [56] "entrezgene"
## [57] "event_type"
## [58] "family"
## [59] "germ_line_variation_source"
## [60] "go_evidence_code"
## [61] "go_id"
## [62] "go_parent_name"
## [63] "go_parent_term"
## [64] "goslim_goa_accession"
## [65] "hgnc_id"
## [66] "hgnc_symbol"
## [67] "hgnc_transcript_name"
## [68] "hpa"
## [69] "illumina_humanht_12_v3"
## [70] "illumina_humanht_12_v4"
## [71] "illumina_humanref_8_v3"
## [72] "illumina_humanwg_6_v1"
## [73] "illumina_humanwg_6_v2"
## [74] "illumina_humanwg_6_v3"
## [75] "interpro"
## [76] "marker_end"
## [77] "marker_start"
## [78] "merops"
## [79] "mim_gene_accession"
## [80] "mim_morbid_accession"
## [81] "mirbase_accession"
## [82] "mirbase_id"
## [83] "mirbase_transcript_name"
## [84] "ottg"
## [85] "ottt"
## [86] "pathology_term"
## [87] "pdb"
## [88] "pfam"
## [89] "phalanx_onearray"
## [90] "phenotype_description"
## [91] "pirsf"
## [92] "prints"
## [93] "profile"
## [94] "protein_id"
## [95] "refseq_mrna"
## [96] "refseq_mrna_predicted"
## [97] "refseq_ncrna"
## [98] "refseq_ncrna_predicted"
## [99] "refseq_peptide"
## [100] "refseq_peptide_predicted"
## [101] "rfam"
## [102] "rfam_transcript_name"
## [103] "shares_cds_and_utr_with_ottt"
## [104] "shares_cds_with_ottt"
## [105] "smart"
## [106] "so_parent_name"
## [107] "somatic_variation_source"
## [108] "source"
## [109] "start"
## [110] "status"
## [111] "strand"
## [112] "superfamily"
## [113] "tigrfam"
## [114] "transcript_count"
## [115] "transcript_source"
## [116] "transcript_status"
## [117] "type"
## [118] "ucsc"
## [119] "unigene"
## [120] "uniparc"
## [121] "uniprot_genename"
## [122] "uniprot_genename_transcript_name"
## [123] "uniprot_sptrembl"
## [124] "uniprot_swissprot"
## [125] "uniprot_swissprot_accession"
## [126] "wikigene_id"
## [127] "wikigene_name"
## [128] "with_affy_hc_g110"
## [129] "with_affy_hg_focus"
## [130] "with_affy_hg_u133_plus_2"
## [131] "with_affy_hg_u133a"
## [132] "with_affy_hg_u133a_2"
## [133] "with_affy_hg_u133b"
## [134] "with_affy_hg_u95a"
## [135] "with_affy_hg_u95av2"
## [136] "with_affy_hg_u95b"
## [137] "with_affy_hg_u95c"
## [138] "with_affy_hg_u95d"
## [139] "with_affy_hg_u95e"
## [140] "with_affy_huex_1_0_st_v2"
## [141] "with_affy_hugene_1_0_st_v1"
## [142] "with_affy_hugene_2_0_st_v1"
## [143] "with_affy_hugenefl"
## [144] "with_affy_primeview"
## [145] "with_affy_u133_x3p"
## [146] "with_agilent_cgh_44b"
## [147] "with_ccds"
## [148] "with_chembl"
## [149] "with_codelink_codelink"
## [150] "with_coil"
## [151] "with_dbass3"
## [152] "with_efg_agilent_sureprint_g3_ge_8x60k"
## [153] "with_efg_agilent_sureprint_g3_ge_8x60k_v2"
## [154] "with_efg_agilent_wholegenome_4x44k_v1"
## [155] "with_efg_agilent_wholegenome_4x44k_v2"
## [156] "with_embl"
## [157] "with_entrezgene"
## [158] "with_exp_atlas_celltype"
## [159] "with_exp_atlas_diseasestate"
## [160] "with_exp_atlas_organismpart"
## [161] "with_exp_est_anatomicalsystem"
## [162] "with_exp_est_associatedwith"
## [163] "with_exp_est_celltype"
## [164] "with_exp_est_developmentstage"
## [165] "with_exp_est_experimentaltechnique"
## [166] "with_exp_est_microarrayplatform"
## [167] "with_exp_est_pathology"
## [168] "with_exp_est_pooling"
## [169] "with_exp_est_tissuepreparation"
## [170] "with_exp_est_treatment"
## [171] "with_go_go"
## [172] "with_go_id"
## [173] "with_hgnc"
## [174] "with_homolog_acar"
## [175] "with_homolog_amel"
## [176] "with_homolog_amex"
## [177] "with_homolog_apla"
## [178] "with_homolog_btau"
## [179] "with_homolog_cele"
## [180] "with_homolog_cfam"
## [181] "with_homolog_chof"
## [182] "with_homolog_cint"
## [183] "with_homolog_cjac"
## [184] "with_homolog_cpor"
## [185] "with_homolog_csav"
## [186] "with_homolog_dmel"
## [187] "with_homolog_dnov"
## [188] "with_homolog_dord"
## [189] "with_homolog_drer"
## [190] "with_homolog_ecab"
## [191] "with_homolog_eeur"
## [192] "with_homolog_etel"
## [193] "with_homolog_falb"
## [194] "with_homolog_fcat"
## [195] "with_homolog_gacu"
## [196] "with_homolog_ggal"
## [197] "with_homolog_ggor"
## [198] "with_homolog_gmor"
## [199] "with_homolog_itri"
## [200] "with_homolog_lafr"
## [201] "with_homolog_lcha"
## [202] "with_homolog_locu"
## [203] "with_homolog_mdom"
## [204] "with_homolog_meug"
## [205] "with_homolog_mfur"
## [206] "with_homolog_mgal"
## [207] "with_homolog_mluc"
## [208] "with_homolog_mmul"
## [209] "with_homolog_mmur"
## [210] "with_homolog_mmus"
## [211] "with_homolog_nleu"
## [212] "with_homolog_oana"
## [213] "with_homolog_oari"
## [214] "with_homolog_ocun"
## [215] "with_homolog_ogar"
## [216] "with_homolog_olat"
## [217] "with_homolog_onil"
## [218] "with_homolog_opri"
## [219] "with_homolog_pabe"
## [220] "with_homolog_pcap"
## [221] "with_homolog_pmar"
## [222] "with_homolog_psin"
## [223] "with_homolog_ptro"
## [224] "with_homolog_pvam"
## [225] "with_homolog_rnor"
## [226] "with_homolog_sara"
## [227] "with_homolog_scer"
## [228] "with_homolog_shar"
## [229] "with_homolog_sscr"
## [230] "with_homolog_tbel"
## [231] "with_homolog_tgut"
## [232] "with_homolog_tnig"
## [233] "with_homolog_trub"
## [234] "with_homolog_tsyr"
## [235] "with_homolog_ttru"
## [236] "with_homolog_vpac"
## [237] "with_homolog_xmac"
## [238] "with_homolog_xtro"
## [239] "with_hpa"
## [240] "with_illumina_humanht_12_v3"
## [241] "with_illumina_humanht_12_v4"
## [242] "with_illumina_humanref_8_v3"
## [243] "with_illumina_humanwg_6_v1"
## [244] "with_illumina_humanwg_6_v2"
## [245] "with_illumina_humanwg_6_v3"
## [246] "with_interpro"
## [247] "with_low_complexity"
## [248] "with_merops"
## [249] "with_mim_gene"
## [250] "with_mim_morbid"
## [251] "with_mirbase"
## [252] "with_ottg"
## [253] "with_ottt"
## [254] "with_ox_arrayexpress"
## [255] "with_ox_clone_based_ensembl_gene"
## [256] "with_ox_clone_based_ensembl_transcript"
## [257] "with_ox_clone_based_vega_gene"
## [258] "with_ox_clone_based_vega_transcript"
## [259] "with_ox_ens_hs_gene"
## [260] "with_ox_ens_hs_transcript"
## [261] "with_ox_ens_hs_translation"
## [262] "with_ox_ens_lrg_gene"
## [263] "with_ox_ens_lrg_transcript"
## [264] "with_ox_goslim_goa"
## [265] "with_ox_hgnc_transcript_name"
## [266] "with_ox_mirbase_transcript_name"
## [267] "with_ox_refseq_mrna"
## [268] "with_ox_refseq_mrna_predicted"
## [269] "with_ox_refseq_ncrna"
## [270] "with_ox_refseq_ncrna_predicted"
## [271] "with_ox_rfam_transcript_name"
## [272] "with_ox_uniparc"
## [273] "with_ox_uniprotsptrembl"
## [274] "with_ox_uniprotswissprot"
## [275] "with_paralog_hsap"
## [276] "with_pdb"
## [277] "with_phalanx_onearray"
## [278] "with_pirsf"
## [279] "with_profile"
## [280] "with_protein_feature_pfam"
## [281] "with_protein_feature_prints"
## [282] "with_protein_id"
## [283] "with_refseq_peptide"
## [284] "with_refseq_peptide_predicted"
## [285] "with_rfamR"
## [286] "with_shares_cds_and_utr_with_ottt"
## [287] "with_shares_cds_with_ottt"
## [288] "with_signal_domain"
## [289] "with_signalp"
## [290] "with_smart"
## [291] "with_superfamily"
## [292] "with_tigrfam"
## [293] "with_tmhmm"
## [294] "with_transmembrane_domain"
## [295] "with_ucsc"
## [296] "with_unigene"
## [297] "with_uniprot_genename"
## [298] "with_uniprot_genename_transcript_name"
## [299] "with_uniprotsptrembl"
## [300] "with_validated_snp"
## [301] "with_wikigene"
filters[grep("start", filters$name), ]
## name description
## 2 start Gene Start (bp)
## 4 band_start Band Start
## 6 marker_start Marker Start
result5 <- getBM(attributes = c("affy_hg_u133_plus_2", "ensembl_gene_id"), filters = c("chromosome_name",
"start", "end"), values = list(chr, start, stop), mart = ensembl)
print(result5)
## affy_hg_u133_plus_2 ensembl_gene_id
## 1 ENSG00000162009
## 2 214555_at ENSG00000162009
## 3 ENSG00000184471
## 4 205845_at ENSG00000196557
## 5 ENSG00000196557
## 6 1557146_a_at ENSG00000261713
## 7 ENSG00000261713
## 8 ENSG00000261720
## 9 ENSG00000181791
## 10 ENSG00000260702
## 11 215502_at ENSG00000260532
## 12 ENSG00000260403
## 13 ENSG00000259910
filters[grep("go", filters$name), ]
## name description
## 43 with_go_id with GO Term Accession(s)
## 88 with_ox_goslim_goa with GOSlim GOA(s)
## 100 with_go_go with GO ID(s)
## 128 go_id GO Term Accession(s) [e.g. GO:0005515]
## 129 goslim_goa_accession GOSlim GOA Accessions(s) [e.g. GO:0005623]
## 199 go_evidence_code GO Evidence code
## 200 go_parent_term Parent term accession
## 201 go_parent_name Parent term name
## 235 with_homolog_ggor Orthologous Gorilla Genes
result6 <- getBM(attributes = c("entrezgene", "hgnc_symbol"), filters = c("go_id"),
values = list("GO:0004707"), mart = ensembl)
print(result6)
## entrezgene hgnc_symbol
## 1 51701 NLK
## 2 5597 MAPK6
## 3 5596 MAPK4
## 4 5599 MAPK8
## 5 5595 MAPK3
## 6 225689 MAPK15
## 7 5598 MAPK7
## 8 1432 MAPK14
## 9 5603 MAPK13
## 10 5594 MAPK1
## 11 5602 MAPK10
## 12 6300 MAPK12
## 13 5600 MAPK11
## 14 5601 MAPK9