From features to annotated gene lists
Overview
Teaching: 15 min
Exercises: 15 minLearning Objectives
Be able to use AnnotationDb methods to association annotations with platform data.
Preparation
To make sure we are doing things right, let’s get the identifiers for 10 probesets.
Try it: Get a limited number of probesets
Let’s work with a limited number of probesets (say, 10) from our differential expression analysis.
topTable()gives us 10 in a data.frame, so we can easily create a character vector of the top 10 probesets using methods from the last episode.Solution
ps <- rownames(topTable(fitted.ebayes))Removing intercept from test coefficientsps[1] "204268_at" "203691_at" "228335_at" "226560_at" "1558846_at" [6] "201820_at" "210809_s_at" "204304_s_at" "204971_at" "206166_s_at"
Annotation of genomic data in AnnotationDb
Using our linear model, we have identified differentially expressed probesets between
our two experimental condition. However, the results from topTable() only shows the
probeset IDs, rather than the gene names. We need to map these
IDs to gene symbols, which can then be further analyzed downstream. Fortunately, R has a
wide range of annotation packages that allows us to do this.
To do so, we will use the annotation package hgu133plus2.db, where hgu133plus2 is the array name. Intuitively, different arrays will have different annotation packages, but they will all end with .db.
Different AnnotationDB packages
Besides platform-specific annotation packages, there are also sequence annotation packages (the BSgenome packages) as well as UCSC transcript packages (the UCSC.knownGenes packages) and the organism annotation packages (the org) packages. Feel free to look up the different annotation packages available on BioConductor under the annotations tab.
Let’s take a look at what’s in the package:
library(hgu133plus2.db)
ls('package:hgu133plus2.db')
[1] "hgu133plus2" "hgu133plus2_dbconn"
[3] "hgu133plus2_dbfile" "hgu133plus2_dbInfo"
[5] "hgu133plus2_dbschema" "hgu133plus2.db"
[7] "hgu133plus2ACCNUM" "hgu133plus2ALIAS2PROBE"
[9] "hgu133plus2CHR" "hgu133plus2CHRLENGTHS"
[11] "hgu133plus2CHRLOC" "hgu133plus2CHRLOCEND"
[13] "hgu133plus2ENSEMBL" "hgu133plus2ENSEMBL2PROBE"
[15] "hgu133plus2ENTREZID" "hgu133plus2ENZYME"
[17] "hgu133plus2ENZYME2PROBE" "hgu133plus2GENENAME"
[19] "hgu133plus2GO" "hgu133plus2GO2ALLPROBES"
[21] "hgu133plus2GO2PROBE" "hgu133plus2MAP"
[23] "hgu133plus2MAPCOUNTS" "hgu133plus2OMIM"
[25] "hgu133plus2ORGANISM" "hgu133plus2ORGPKG"
[27] "hgu133plus2PATH" "hgu133plus2PATH2PROBE"
[29] "hgu133plus2PFAM" "hgu133plus2PMID"
[31] "hgu133plus2PMID2PROBE" "hgu133plus2PROSITE"
[33] "hgu133plus2REFSEQ" "hgu133plus2SYMBOL"
[35] "hgu133plus2UNIPROT"
This version of ls() allows us to quickly list the contents of any package. What we see are a
bunch of maps from the hgu133plus2 probeset identifiers (which we have) to other identifiers
(which we don’t). We need to provide the probe identifiers of interest and then retrieve the other
identifiers of interest.
Method 1: reaching into the databases
Now that we have the probesets in a character vector, let’s use what we have. Each of the objects in ls('package:hgu133plus2') is an environment, which is a special kind of list. The way to extract the values we want is to use the function mget() with the probsets as an argument. If we want the result to be a vector, we need to unlist() it. Here’s an example.
## get the symbols for our probesets
unlist(mget(ps,hgu133plus2SYMBOL))
204268_at 203691_at 228335_at 226560_at 1558846_at 201820_at
"S100A2" "PI3" "CLDN11" "SGPP2" "PNLIPRP3" "KRT5"
210809_s_at 204304_s_at 204971_at 206166_s_at
"POSTN" "PROM1" "CSTA" "CLCA2"
This method works on all such annotation data packages, but is a bit cumbersome. Very often we want more than one piece of information, and unlisting might be dangerous if the mapping is not one-to-one.
Let’s try a better method.
Method 2: The AnnotationDbi interface
A lot of Annotation data packages use a common interface through the AnnotationDbi package (see the vignette). There are four key functions:
select()- run a query for selected columns with selected keys
columns()- identify what columns are available for a database
keytypes()- some, but occasionally not all, of the columns can be used as keys for a query
keys()- list the keys
Let’s first look at the available columns for our chip
columns(hgu133plus2.db)
[1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS"
[6] "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL" "GENENAME"
[11] "GENETYPE" "GO" "GOALL" "IPI" "MAP"
[16] "OMIM" "ONTOLOGY" "ONTOLOGYALL" "PATH" "PFAM"
[21] "PMID" "PROBEID" "PROSITE" "REFSEQ" "SYMBOL"
[26] "UCSCKG" "UNIPROT"
We have a lot of columns to choose from. How about which can be used as keys
keytypes(hgu133plus2.db)
[1] "ACCNUM" "ALIAS" "ENSEMBL" "ENSEMBLPROT" "ENSEMBLTRANS"
[6] "ENTREZID" "ENZYME" "EVIDENCE" "EVIDENCEALL" "GENENAME"
[11] "GENETYPE" "GO" "GOALL" "IPI" "MAP"
[16] "OMIM" "ONTOLOGY" "ONTOLOGYALL" "PATH" "PFAM"
[21] "PMID" "PROBEID" "PROSITE" "REFSEQ" "SYMBOL"
[26] "UCSCKG" "UNIPROT"
It looks like all the columns can be used as keys. One of the key types is “PROBEID”. That looks right.
head(keys(hgu133plus2.db,keytype="PROBEID"))
[1] "1007_s_at" "1053_at" "117_at" "121_at" "1255_g_at" "1294_at"
If we want to extract the symbols, gene identifiers, and gene names, it’s as simple as using the
select() function from AnnotationDbi with the probesets as our identifiers:
AnnotationDbi::select(hgu133plus2.db,ps,c("SYMBOL","ENTREZID","GENENAME"),keytype="PROBEID")
'select()' returned 1:1 mapping between keys and columns
PROBEID SYMBOL ENTREZID GENENAME
1 204268_at S100A2 6273 S100 calcium binding protein A2
2 203691_at PI3 5266 peptidase inhibitor 3
3 228335_at CLDN11 5010 claudin 11
4 226560_at SGPP2 130367 sphingosine-1-phosphate phosphatase 2
5 1558846_at PNLIPRP3 119548 pancreatic lipase related protein 3
6 201820_at KRT5 3852 keratin 5
7 210809_s_at POSTN 10631 periostin
8 204304_s_at PROM1 8842 prominin 1
9 204971_at CSTA 1475 cystatin A
10 206166_s_at CLCA2 9635 chloride channel accessory 2
Try it!
Using the given information, use
topTable()to retrieve all genes that are differentially expressed with a adjusted p-value of less than 0.05, with at fold change of at least two (log fold change at least one). Restrict yourself to upregulated genes.Solution
ps2 <- topTable(fitted.ebayes,number=Inf,p.value = 0.05,lfc=1)Removing intercept from test coefficientsps2_up <- rownames(ps2[ps2$logFC > 0,]) df <- AnnotationDbi::select(hgu133plus2.db,ps2_up,c("SYMBOL","ENTREZID","GENENAME"),keytype="PROBEID")'select()' returned 1:many mapping between keys and columnsdplyr::mutate(df,GENENAME=stringr::str_trunc(GENENAME,30))PROBEID SYMBOL ENTREZID GENENAME 1 228335_at CLDN11 5010 claudin 11 2 210809_s_at POSTN 10631 periostin 3 211959_at IGFBP5 3488 insulin like growth factor ... 4 223618_at FMN2 56776 formin 2 5 210143_at ANXA10 11199 annexin A10 6 203083_at THBS2 7058 thrombospondin 2 7 227919_at UCA1 652995 urothelial cancer associated 1 8 235521_at HOXA3 3200 homeobox A3 9 213069_at HEG1 57493 heart development protein w... 10 210095_s_at IGFBP3 3486 insulin like growth factor ... 11 1555778_a_at POSTN 10631 periostin 12 227450_at ERP27 121506 endoplasmic reticulum prote... 13 203504_s_at ABCA1 19 ATP binding cassette subfam... 14 229824_at SHC3 53358 SHC adaptor protein 3 15 201744_s_at LUM 4060 lumican 16 203440_at CDH2 1000 cadherin 2 17 203854_at CFI 3426 complement factor I 18 242005_at <NA> <NA> <NA> 19 215729_s_at VGLL1 51442 vestigial like family member 1 20 202481_at DHRS3 9249 dehydrogenase/reductase 3 21 203304_at BAMBI 25805 BMP and activin membrane bo... 22 202363_at SPOCK1 6695 SPARC (osteonectin), cwcv a... 23 225202_at RHOBTB3 22836 Rho related BTB domain cont... 24 1555471_a_at FMN2 56776 formin 2 25 200665_s_at SPARC 6678 secreted protein acidic and... 26 227396_at PTPRJ 5795 protein tyrosine phosphatas... 27 223204_at GASK1B 51313 golgi associated kinase 1B 28 203108_at GPRC5A 9052 G protein-coupled receptor ... 29 206336_at CXCL6 6372 C-X-C motif chemokine ligand 6 30 204422_s_at FGF2 2247 fibroblast growth factor 2 31 223557_s_at TMEFF2 23671 transmembrane protein with ... 32 231579_s_at TIMP2 7077 TIMP metallopeptidase inhib... 33 214954_at SUSD5 26032 sushi domain containing 5 34 226279_at PRSS23 11098 serine protease 23 35 236277_at <NA> <NA> <NA> 36 223484_at C15orf48 84419 chromosome 15 open reading ... 37 203874_s_at SMARCA1 6594 SWI/SNF related, matrix ass... 38 224480_s_at GPAT3 84803 glycerol-3-phosphate acyltr... 39 213258_at TFPI 7035 tissue factor pathway inhib... 40 218435_at DNAJC15 29103 DnaJ heat shock protein fam... 41 202016_at MEST 4232 mesoderm specific transcript 42 210762_s_at DLC1 10395 DLC1 Rho GTPase activating ... 43 226905_at RFLNB 359845 refilin B 44 231240_at DIO2 1734 iodothyronine deiodinase 2 45 203505_at ABCA1 19 ATP binding cassette subfam... 46 202838_at FUCA1 2517 alpha-L-fucosidase 1 47 201288_at ARHGDIB 397 Rho GDP dissociation inhibi... 48 221024_s_at SLC2A10 81031 solute carrier family 2 mem... 49 203180_at ALDH1A3 220 aldehyde dehydrogenase 1 fa... 50 234994_at TMEM200A 114801 transmembrane protein 200A 51 212328_at LIMCH1 22998 LIM and calponin homology d... 52 229242_at TNFSF15 9966 TNF superfamily member 15 53 212667_at SPARC 6678 secreted protein acidic and... 54 218332_at BEX1 55859 brain expressed X-linked 1 55 206392_s_at RARRES1 5918 retinoic acid receptor resp... 56 212143_s_at IGFBP3 3486 insulin like growth factor ... 57 230869_at FAM155A 728215 family with sequence simila... 58 1562484_at MEIOC 284071 meiosis specific with coile... 59 208510_s_at PPARG 5468 peroxisome proliferator act... 60 209291_at ID4 3400 inhibitor of DNA binding 4,... 61 238689_at ADGRF1 266977 adhesion G protein-coupled ... 62 202391_at BASP1 10409 brain abundant membrane att... 63 203895_at PLCB4 5332 phospholipase C beta 4 64 212325_at LIMCH1 22998 LIM and calponin homology d... 65 225645_at EHF 26298 ETS homologous factor 66 201565_s_at ID2 3398 inhibitor of DNA binding 2 67 206391_at RARRES1 5918 retinoic acid receptor resp... 68 215294_s_at SMARCA1 6594 SWI/SNF related, matrix ass... 69 225817_at CGNL1 84952 cingulin like 1 70 201566_x_at ID2 3398 inhibitor of DNA binding 2 71 207826_s_at ID3 3399 inhibitor of DNA binding 3,... 72 221085_at TNFSF15 9966 TNF superfamily member 15 73 226751_at CNRIP1 25927 cannabinoid receptor intera... 74 232231_at RUNX2 860 RUNX family transcription f... 75 223315_at NTN4 59277 netrin 4 76 203851_at IGFBP6 3489 insulin like growth factor ... 77 204421_s_at FGF2 2247 fibroblast growth factor 2 78 212327_at LIMCH1 22998 LIM and calponin homology d... 79 202957_at HCLS1 3059 hematopoietic cell-specific... 80 206382_s_at BDNF 627 brain derived neurotrophic ... 81 209581_at PLAAT3 11145 phospholipase A and acyltra... 82 203603_s_at ZEB2 9839 zinc finger E-box binding h... 83 204159_at CDKN2C 1031 cyclin dependent kinase inh... 84 209121_x_at NR2F2 7026 nuclear receptor subfamily ... 85 204341_at TRIM16 10626 tripartite motif containing 16 86 204070_at PLAAT4 5920 phospholipase A and acyltra... 87 1566766_a_at MACC1 346389 MET transcriptional regulat... 88 1555812_a_at ARHGDIB 397 Rho GDP dissociation inhibi... 89 219014_at PLAC8 51316 placenta associated 8 90 225673_at MYADM 91663 myeloid associated differen... 91 212148_at PBX1 5087 PBX homeobox 1 92 205923_at RELN 5649 reelin 93 207480_s_at MEIS2 4212 Meis homeobox 2 94 201859_at SRGN 5552 serglycin 95 213170_at GPX7 2882 glutathione peroxidase 7 96 243366_s_at ITGA4 3676 integrin subunit alpha 4 97 212444_at GPRC5A 9052 G protein-coupled receptor ... 98 235004_at RBM24 221662 RNA binding motif protein 24 99 215073_s_at NR2F2 7026 nuclear receptor subfamily ... 100 212233_at MAP1B 4131 microtubule associated prot... 101 206307_s_at FOXD1 2297 forkhead box D1 102 220468_at ARL14 80117 ADP ribosylation factor lik... 103 213338_at TMEM158 25907 transmembrane protein 158 104 202524_s_at SPOCK2 9806 SPARC (osteonectin), cwcv a... 105 206595_at CST6 1474 cystatin E/M 106 223103_at STARD10 10809 StAR related lipid transfer... 107 202458_at PRSS23 11098 serine protease 23 108 202976_s_at RHOBTB3 22836 Rho related BTB domain cont... 109 205487_s_at VGLL1 51442 vestigial like family member 1 110 202732_at PKIG 11142 cAMP-dependent protein kina... 111 230250_at PTPRB 5787 protein tyrosine phosphatas... 112 226622_at MUC20 200958 mucin 20, cell surface asso... 113 204086_at PRAME 23532 PRAME nuclear receptor tran... 114 228640_at PCDH7 5099 protocadherin 7 115 213620_s_at ICAM2 3384 intercellular adhesion mole... 116 228573_at ANTXR2 118429 ANTXR cell adhesion molecule 2 117 204256_at ELOVL6 79071 ELOVL fatty acid elongase 6 118 223044_at SLC40A1 30061 solute carrier family 40 me... 119 203700_s_at DIO2 1734 iodothyronine deiodinase 2 120 232235_at DSEL 92126 dermatan sulfate epimerase ... 121 201042_at TGM2 7052 transglutaminase 2 122 203167_at TIMP2 7077 TIMP metallopeptidase inhib... 123 201939_at PLK2 10769 polo like kinase 2 124 227123_at RAB3B 5865 RAB3B, member RAS oncogene ... 125 209035_at MDK 4192 midkine 126 204932_at TNFRSF11B 4982 TNF receptor superfamily me... 127 227764_at LYPD6 130574 LY6/PLAUR domain containing 6 128 215446_s_at LOX 4015 lysyl oxidase 129 203828_s_at IL32 9235 interleukin 32 130 202202_s_at LAMA4 3910 laminin subunit alpha 4 131 205422_s_at ITGBL1 9358 integrin subunit beta like 1 132 205844_at VNN1 8876 vanin 1 133 231849_at KRT80 144501 keratin 80 134 203510_at MET 4233 MET proto-oncogene, recepto... 135 203875_at SMARCA1 6594 SWI/SNF related, matrix ass... 136 215617_at SPATS2L 26010 spermatogenesis associated ... 137 203767_s_at STS 412 steroid sulfatase 138 232676_x_at MYEF2 50804 myelin expression factor 2 139 227811_at FGD3 89846 FYVE, RhoGEF and PH domain ... 140 212096_s_at MTUS1 57509 microtubule associated scaf... 141 213416_at ITGA4 3676 integrin subunit alpha 4 142 209470_s_at GPM6A 2823 glycoprotein M6A 143 224560_at TIMP2 7077 TIMP metallopeptidase inhib... 144 225061_at DNAJA4 55466 DnaJ heat shock protein fam... 145 219179_at DACT1 51339 dishevelled binding antagon... 146 212764_at ZEB1 6935 zinc finger E-box binding h... 147 210220_at FZD2 2535 frizzled class receptor 2 148 219937_at TRHDE 29953 thyrotropin releasing hormo... 149 203896_s_at PLCB4 5332 phospholipase C beta 4 150 213358_at MTCL1 23255 microtubule crosslinking fa... 151 221872_at RARRES1 5918 retinoic acid receptor resp... 152 218284_at SMAD3 4088 SMAD family member 3 153 204149_s_at GSTM4 2948 glutathione S-transferase mu 4 154 212822_at HEG1 57493 heart development protein w... 155 212489_at COL5A1 1289 collagen type V alpha 1 chain 156 201280_s_at DAB2 1601 DAB adaptor protein 2 157 1555564_a_at CFI 3426 complement factor I 158 1557779_at LNCAROD 101928687 lncRNA activating regulator... 159 207463_x_at PRSS3 5646 serine protease 3 160 216048_s_at RHOBTB3 22836 Rho related BTB domain cont... 161 227688_at LRCH2 57631 leucine rich repeats and ca... 162 224352_s_at CFL2 1073 cofilin 2 163 203697_at FRZB 2487 frizzled related protein 164 208937_s_at ID1 3397 inhibitor of DNA binding 1,... 165 204667_at FOXA1 3169 forkhead box A1 166 213711_at KRT81 3887 keratin 81 167 201010_s_at TXNIP 10628 thioredoxin interacting pro... 168 202554_s_at GSTM3 2947 glutathione S-transferase mu 3 169 208712_at CCND1 595 cyclin D1 170 214091_s_at GPX3 2878 glutathione peroxidase 3 171 1556300_s_at SIM1 6492 SIM bHLH transcription fact... 172 232151_at MACC1 346389 MET transcriptional regulat... 173 205387_s_at CGB3 1082 chorionic gonadotropin subu... 174 205387_s_at CGB5 93659 chorionic gonadotropin subu... 175 205387_s_at CGB7 94027 chorionic gonadotropin subu... 176 226084_at MAP1B 4131 microtubule associated prot... 177 243521_at ZXDA 7789 zinc finger X-linked duplic... 178 203325_s_at COL5A1 1289 collagen type V alpha 1 chain 179 212509_s_at MXRA7 439921 matrix remodeling associated 7 180 221577_x_at GDF15 9518 growth differentiation fact... 181 212386_at TCF4 6925 transcription factor 4 182 205016_at TGFA 7039 transforming growth factor ... 183 228642_at HOTAIRM1 100506311 HOXA transcript antisense R... 184 235256_s_at GALM 130589 galactose mutarotase 185 226997_at ADAMTS12 81792 ADAM metallopeptidase with ... 186 213906_at MYBL1 4603 MYB proto-oncogene like 1 187 221911_at ETV1 2115 ETS variant transcription f... 188 221031_s_at APOLD1 81575 apolipoprotein L domain con... 189 226713_at CCDC50 152137 coiled-coil domain containi... 190 228005_at ZXDB 158586 zinc finger X-linked duplic... 191 202800_at SLC1A3 6507 solute carrier family 1 mem... 192 236831_at CCDC50 152137 coiled-coil domain containi... 193 204036_at LPAR1 1902 lysophosphatidic acid recep... 194 225524_at ANTXR2 118429 ANTXR cell adhesion molecule 2 195 212339_at EPB41L1 2036 erythrocyte membrane protei... 196 225003_at TMEM205 374882 transmembrane protein 205 197 244353_s_at SLC2A12 154091 solute carrier family 2 mem... 198 209120_at NR2F2 7026 nuclear receptor subfamily ... 199 203184_at FBN2 2201 fibrillin 2 200 209267_s_at SLC39A8 64116 solute carrier family 39 me... 201 212067_s_at C1R 715 complement C1r 202 224663_s_at CFL2 1073 cofilin 2 203 1557051_s_at HOTAIRM1 100506311 HOXA transcript antisense R... 204 227599_at MB21D2 151963 Mab-21 domain containing 2 205 238029_s_at SLC16A14 151473 solute carrier family 16 me... 206 228693_at CCDC50 152137 coiled-coil domain containi... 207 227966_s_at CCDC74A 90557 coiled-coil domain containi... 208 227966_s_at CCDC74B 91409 coiled-coil domain containi... 209 230130_at SLIT2 9353 slit guidance ligand 2 210 237435_at <NA> <NA> <NA> 211 235591_at SSTR1 6751 somatostatin receptor 1 212 203632_s_at GPRC5B 51704 G protein-coupled receptor ... 213 239202_at RAB3B 5865 RAB3B, member RAS oncogene ... 214 1555852_at PSMB8-AS1 100507463 PSMB8 antisense RNA 1 (head... 215 235230_at PLCXD2 257068 phosphatidylinositol specif... 216 203060_s_at PAPSS2 9060 3'-phosphoadenosine 5'-phos... 217 229269_x_at SSBP4 170463 single stranded DNA binding... 218 227444_at ARMCX4 100131755 armadillo repeat containing... 219 205535_s_at PCDH7 5099 protocadherin 7 220 203939_at NT5E 4907 5'-nucleotidase ecto 221 229194_at PCGF5 84333 polycomb group ring finger 5 222 213413_at STON1 11037 stonin 1 223 204908_s_at BCL3 602 BCL3 transcription coactivator 224 202179_at BLMH 642 bleomycin hydrolase 225 203585_at ZNF185 7739 zinc finger protein 185 wit... 226 222803_at PRTFDC1 56952 phosphoribosyl transferase ... 227 228737_at TOX2 84969 TOX high mobility group box... 228 203636_at MID1 4281 midline 1 229 228107_at C8orf88 100127983 chromosome 8 open reading f... 230 202664_at WIPF1 7456 WAS/WASL interacting protei... 231 228098_s_at MYLIP 29116 myosin regulatory light cha... 232 213400_s_at TBL1X 6907 transducin beta like 1 X-li... 233 213421_x_at PRSS3 5646 serine protease 3 234 212423_at ZCCHC24 219654 zinc finger CCHC-type conta... 235 213150_at HOXA10 3206 homeobox A10 236 204339_s_at RGS4 5999 regulator of G protein sign... 237 204994_at MX2 4600 MX dynamin like GTPase 2 238 204237_at GULP1 51454 GULP PTB domain containing ... 239 214639_s_at HOXA1 3198 homeobox A1 240 201348_at GPX3 2878 glutathione peroxidase 3 241 204337_at RGS4 5999 regulator of G protein sign... 242 235050_at SLC2A12 154091 solute carrier family 2 mem... 243 204338_s_at RGS4 5999 regulator of G protein sign... 244 202388_at RGS2 5997 regulator of G protein sign... 245 1566764_at MACC1 346389 MET transcriptional regulat... 246 208782_at FSTL1 11167 follistatin like 1 247 210664_s_at TFPI 7035 tissue factor pathway inhib... 248 219895_at TMEM255A 55026 transmembrane protein 255A 249 204748_at PTGS2 5743 prostaglandin-endoperoxide ... 250 204298_s_at LOX 4015 lysyl oxidase 251 227719_at SMAD9 4093 SMAD family member 9 252 204819_at FGD1 2245 FYVE, RhoGEF and PH domain ... 253 219902_at BHMT2 23743 betaine--homocysteine S-met... 254 200999_s_at CKAP4 10970 cytoskeleton associated pro... 255 226137_at ZFHX3 463 zinc finger homeobox 3 256 228933_at NHS 4810 NHS actin remodeling regulator 257 233825_s_at CD99L2 83692 CD99 molecule like 2 258 227846_at GPR176 11245 G protein-coupled receptor 176 259 242417_at PLEKHA7 144100 pleckstrin homology domain ... 260 201058_s_at MYL9 10398 myosin light chain 9 261 228128_x_at PAPPA 5069 pappalysin 1 262 204955_at SRPX 8406 sushi repeat containing pro... 263 209198_s_at SYT11 23208 synaptotagmin 11 264 201506_at TGFBI 7045 transforming growth factor ... 265 209356_x_at EFEMP2 30008 EGF containing fibulin extr... 266 203441_s_at CDH2 1000 cadherin 2 267 223218_s_at NFKBIZ 64332 NFKB inhibitor zeta 268 205316_at SLC15A2 6565 solute carrier family 15 me... 269 215263_at ZXDA 7789 zinc finger X-linked duplic... 270 215263_at ZXDB 158586 zinc finger X-linked duplic... 271 232239_at LINC00865 643529 long intergenic non-protein... 272 212531_at LCN2 3934 lipocalin 2 273 213844_at HOXA5 3202 homeobox A5 274 210065_s_at UPK1B 7348 uroplakin 1B 275 227458_at CD274 29126 CD274 molecule 276 230372_at HAS2 3037 hyaluronan synthase 2 277 200962_at RPL31 6160 ribosomal protein L31 278 218573_at MAGEH1 28986 MAGE family member H1 279 242051_at <NA> <NA> <NA> 280 226152_at TTC7B 145567 tetratricopeptide repeat do... 281 229437_at MIR155HG 114614 MIR155 host gene 282 209676_at TFPI 7035 tissue factor pathway inhib... 283 205884_at ITGA4 3676 integrin subunit alpha 4 284 204639_at ADA 100 adenosine deaminase 285 1554171_at ZMYM3 9203 zinc finger MYM-type contai... 286 235391_at CIBAR1 137392 CBY1 interacting BAR domain... 287 205398_s_at SMAD3 4088 SMAD family member 3 288 234192_s_at GKAP1 80318 G kinase anchoring protein 1 289 222016_s_at ZSCAN31 64288 zinc finger and SCAN domain... 290 222942_s_at TIAM2 26230 TIAM Rac1 associated GEF 2 291 219450_at C4orf19 55286 chromosome 4 open reading f... 292 210064_s_at UPK1B 7348 uroplakin 1B 293 218729_at LXN 56925 latexin 294 229461_x_at NEGR1 257194 neuronal growth regulator 1 295 230788_at GCNT2 2651 glucosaminyl (N-acetyl) tra... 296 209651_at TGFB1I1 7041 transforming growth factor ... 297 206116_s_at TPM1 7168 tropomyosin 1 298 229354_at PDCD6-AHRR 116412618 PDCD6-AHRR readthrough (NMD... 299 229354_at AHRR 57491 aryl-hydrocarbon receptor r... 300 226876_at RFLNB 359845 refilin B 301 241484_x_at FRG1CP 100289097 FSHD region gene 1 family m... 302 226875_at DOCK11 139818 dedicator of cytokinesis 11 303 238032_at <NA> <NA> <NA> 304 204279_at PSMB9 5698 proteasome 20S subunit beta 9 305 224823_at MYLK 4638 myosin light chain kinase 306 226534_at KITLG 4254 KIT ligand 307 242093_at SYTL5 94122 synaptotagmin like 5 308 224990_at SMIM14 201895 small integral membrane pro... 309 232322_x_at STARD10 10809 StAR related lipid transfer... 310 204933_s_at TNFRSF11B 4982 TNF receptor superfamily me... 311 201510_at ELF3 1999 E74 like ETS transcription ... 312 205130_at MOK 5891 MOK protein kinase 313 1557961_s_at C8orf88 100127983 chromosome 8 open reading f... 314 205259_at NR3C2 4306 nuclear receptor subfamily ... 315 206432_at HAS2 3037 hyaluronan synthase 2 316 201009_s_at TXNIP 10628 thioredoxin interacting pro... 317 219148_at PBK 55872 PDZ binding kinase 318 229465_s_at <NA> <NA> <NA> 319 227503_at <NA> <NA> <NA> 320 205978_at KL 9365 klotho 321 210751_s_at RGN 9104 regucalcin 322 214519_s_at RLN2 6019 relaxin 2 323 225847_at NCEH1 57552 neutral cholesterol ester h... 324 227449_at EPHA4 2043 EPH receptor A4 325 222772_at MYEF2 50804 myelin expression factor 2 326 220979_s_at ST6GALNAC5 81849 ST6 N-acetylgalactosaminide... 327 228035_at STK33 65975 serine/threonine kinase 33 328 235171_at LOC100505501 100505501 uncharacterized LOC100505501 329 238423_at SYTL3 94120 synaptotagmin like 3 330 215913_s_at GULP1 51454 GULP PTB domain containing ... 331 209292_at ID4 3400 inhibitor of DNA binding 4,... 332 203699_s_at DIO2 1734 iodothyronine deiodinase 2 333 210868_s_at ELOVL6 79071 ELOVL fatty acid elongase 6 334 206698_at XK 7504 X-linked Kx blood group 335 226066_at MITF 4286 melanocyte inducing transcr... 336 210002_at GATA6 2627 GATA binding protein 6 337 212771_at FAM171A1 221061 family with sequence simila... 338 227491_at ELOVL6 79071 ELOVL fatty acid elongase 6 339 209293_x_at ID4 3400 inhibitor of DNA binding 4,... 340 214651_s_at HOXA9 3205 homeobox A9 341 214651_s_at HOXA10-HOXA9 100534589 HOXA10-HOXA9 readthrough 342 204037_at LPAR1 1902 lysophosphatidic acid recep... 343 224964_s_at GNG2 54331 G protein subunit gamma 2 344 228450_at PLEKHA7 144100 pleckstrin homology domain ... 345 226425_at CLIP4 79745 CAP-Gly domain containing l... 346 237086_at FOXA1 3169 forkhead box A1 347 205890_s_at UBD 10537 ubiquitin D 348 205890_s_at GABBR1 2550 gamma-aminobutyric acid typ... 349 232079_s_at NECTIN2 5819 nectin cell adhesion molecu... 350 229092_at NR2F2 7026 nuclear receptor subfamily ... 351 227341_at BEND7 222389 BEN domain containing 7 352 212488_at COL5A1 1289 collagen type V alpha 1 chain 353 238877_at EYA4 2070 EYA transcriptional coactiv... 354 228850_s_at SLIT2 9353 slit guidance ligand 2 355 205925_s_at RAB3B 5865 RAB3B, member RAS oncogene ... 356 1554062_at XG 7499 Xg glycoprotein (Xg blood g... 357 201150_s_at TIMP3 7078 TIMP metallopeptidase inhib... 358 207177_at PTGFR 5737 prostaglandin F receptor 359 236918_s_at LRRC34 151827 leucine rich repeat contain... 360 227554_at MAGI2-AS3 100505881 MAGI2 antisense RNA 3 361 205005_s_at NMT2 9397 N-myristoyltransferase 2 362 201425_at ALDH2 217 aldehyde dehydrogenase 2 fa... 363 210675_s_at PTPRR 5801 protein tyrosine phosphatas... 364 227703_s_at SYTL4 94121 synaptotagmin like 4 365 52837_at SHISAL1 85352 shisa like 1 366 226326_at PCGF5 84333 polycomb group ring finger 5 367 209782_s_at DBP 1628 D-box binding PAR bZIP tran... 368 227763_at LYPD6 130574 LY6/PLAUR domain containing 6 369 212636_at QKI 9444 QKI, KH domain containing R... 370 35626_at SGSH 6448 N-sulfoglucosamine sulfohyd... 371 222771_s_at MYEF2 50804 myelin expression factor 2 372 220014_at PRR16 51334 proline rich 16 373 201008_s_at TXNIP 10628 thioredoxin interacting pro... 374 226933_s_at ID4 3400 inhibitor of DNA binding 4,... 375 228608_at NALCN 259232 sodium leak channel, non-se... 376 201278_at DAB2 1601 DAB adaptor protein 2 377 212151_at PBX1 5087 PBX homeobox 1 378 201137_s_at HLA-DPB1 3115 major histocompatibility co... 379 204646_at DPYD 1806 dihydropyrimidine dehydroge... 380 212336_at EPB41L1 2036 erythrocyte membrane protei... 381 236769_at <NA> <NA> <NA> 382 203637_s_at MID1 4281 midline 1 383 229480_at MAGI2-AS3 100505881 MAGI2 antisense RNA 3 384 201069_at MMP2 4313 matrix metallopeptidase 2 385 211458_s_at GABARAPL3 23766 GABA type A receptor associ... 386 211458_s_at GABARAPL1 23710 GABA type A receptor associ... 387 235988_at ADGRF1 266977 adhesion G protein-coupled ... 388 201809_s_at ENG 2022 endoglin 389 216014_s_at ZXDA 7789 zinc finger X-linked duplic... 390 216014_s_at ZXDB 158586 zinc finger X-linked duplic... 391 205924_at RAB3B 5865 RAB3B, member RAS oncogene ... 392 204235_s_at GULP1 51454 GULP PTB domain containing ... 393 214033_at ABCC6 368 ATP binding cassette subfam... 394 214033_at ABCC6P1 653190 ATP binding cassette subfam... 395 214033_at ABCC6P2 730013 ATP binding cassette subfam... 396 224941_at PAPPA 5069 pappalysin 1 397 206029_at ANKRD1 27063 ankyrin repeat domain 1 398 201858_s_at SRGN 5552 serglycin 399 206580_s_at EFEMP2 30008 EGF containing fibulin extr... 400 207836_s_at RBPMS 11030 RNA binding protein, mRNA p... 401 217388_s_at KYNU 8942 kynureninase 402 209710_at GATA2 2624 GATA binding protein 2 403 203196_at ABCC4 10257 ATP binding cassette subfam... 404 204529_s_at TOX 9760 thymocyte selection associa... 405 241789_at RBMS3 27303 RNA binding motif single st... 406 235759_at <NA> <NA> <NA> 407 1554334_a_at DNAJA4 55466 DnaJ heat shock protein fam... 408 202975_s_at RHOBTB3 22836 Rho related BTB domain cont... 409 212093_s_at MTUS1 57509 microtubule associated scaf... 410 202087_s_at CTSL 1514 cathepsin L 411 235051_at CCDC50 152137 coiled-coil domain containi... 412 209897_s_at SLIT2 9353 slit guidance ligand 2 413 233496_s_at CFL2 1073 cofilin 2 414 205885_s_at ITGA4 3676 integrin subunit alpha 4 415 235367_at MYPN 84665 myopalladin 416 218469_at GREM1 26585 gremlin 1, DAN family BMP a... 417 1552502_s_at RHBDL2 54933 rhomboid like 2 418 227486_at NT5E 4907 5'-nucleotidase ecto 419 238447_at RBMS3 27303 RNA binding motif single st... 420 205006_s_at NMT2 9397 N-myristoyltransferase 2 421 231941_s_at MUC20 200958 mucin 20, cell surface asso... 422 241869_at APOL6 80830 apolipoprotein L6 423 218885_s_at GALNT12 79695 polypeptide N-acetylgalacto... 424 231841_s_at JCAD 57608 junctional cadherin 5 assoc... 425 59697_at RAB15 376267 RAB15, member RAS oncogene ... 426 1554997_a_at PTGS2 5743 prostaglandin-endoperoxide ... 427 238983_at NSUN7 79730 NOP2/Sun RNA methyltransfer... 428 225978_at RIMKLB 57494 ribosomal modification prot... 429 225242_s_at CCDC80 151887 coiled-coil domain containi... 430 218468_s_at GREM1 26585 gremlin 1, DAN family BMP a... 431 231842_at JCAD 57608 junctional cadherin 5 assoc... 432 226603_at SAMD9L 219285 sterile alpha motif domain ... 433 203886_s_at FBLN2 2199 fibulin 2 434 230720_at RNF182 221687 ring finger protein 182 435 213640_s_at LOX 4015 lysyl oxidase 436 229441_at PRSS23 11098 serine protease 23 437 211990_at HLA-DPA1 3113 major histocompatibility co... 438 214457_at HOXA2 3199 homeobox A2 439 214825_at FAM155A 728215 family with sequence simila... 440 202531_at IRF1 3659 interferon regulatory factor 1 441 223723_at MELTF 4241 melanotransferrin 442 1553997_a_at ASPHD1 253982 aspartate beta-hydroxylase ... 443 232270_at AOPEP 84909 aminopeptidase O (putative) 444 213158_at ZBTB20 26137 zinc finger and BTB domain ... 445 232361_s_at EHF 26298 ETS homologous factor 446 209469_at GPM6A 2823 glycoprotein M6A 447 221232_s_at ANKRD2 26287 ankyrin repeat domain 2 448 213547_at CAND2 23066 cullin associated and neddy... 449 214247_s_at DKK3 27122 dickkopf WNT signaling path... 450 202555_s_at MYLK 4638 myosin light chain kinase 451 224189_x_at EHF 26298 ETS homologous factor 452 204726_at CDH13 1012 cadherin 13 453 204115_at GNG11 2791 G protein subunit gamma 11 454 210176_at TLR1 7096 toll like receptor 1 455 218029_at RIPOR1 79567 RHO family interacting cell... 456 210757_x_at DAB2 1601 DAB adaptor protein 2 457 235350_at C4orf19 55286 chromosome 4 open reading f... 458 223253_at EPDR1 54749 ependymin related 1 459 200998_s_at CKAP4 10970 cytoskeleton associated pro... 460 206291_at NTS 4922 neurotensin 461 214078_at PAK3 5063 p21 (RAC1) activated kinase 3 462 211003_x_at TGM2 7052 transglutaminase 2 463 201279_s_at DAB2 1601 DAB adaptor protein 2 464 218613_at PSD3 23362 pleckstrin and Sec7 domain ... 465 204284_at PPP1R3C 5507 protein phosphatase 1 regul... 466 209159_s_at NDRG4 65009 NDRG family member 4 467 218893_at ISOC2 79763 isochorismatase domain cont... 468 219944_at CLIP4 79745 CAP-Gly domain containing l... 469 204198_s_at RUNX3 864 RUNX family transcription f... 470 203058_s_at PAPSS2 9060 3'-phosphoadenosine 5'-phos... 471 232825_s_at DSEL 92126 dermatan sulfate epimerase ... 472 226103_at NEXN 91624 nexilin F-actin binding pro... 473 243041_s_at <NA> <NA> <NA> 474 1555097_a_at PTGFR 5737 prostaglandin F receptor 475 1568838_at WASIR2 100132169 WASH and IL9R antisense RNA 2 476 224940_s_at PAPPA 5069 pappalysin 1 477 235570_at RBMS3 27303 RNA binding motif single st... 478 201482_at QSOX1 5768 quiescin sulfhydryl oxidase 1 479 203698_s_at FRZB 2487 frizzled related protein 480 223614_at MMP16 4325 matrix metallopeptidase 16 481 211573_x_at TGM2 7052 transglutaminase 2 482 201147_s_at TIMP3 7078 TIMP metallopeptidase inhib... 483 202724_s_at FOXO1 2308 forkhead box O1 484 206600_s_at SLC16A5 9121 solute carrier family 16 me... 485 226771_at ATP8B2 57198 ATPase phospholipid transpo... 486 225562_at RASA3 22821 RAS p21 protein activator 3 487 211599_x_at MET 4233 MET proto-oncogene, recepto... 488 228360_at LYPD6B 130576 LY6/PLAUR domain containing 6B 489 1559506_x_at MIR137HG 400765 MIR137 host gene 490 1559506_x_at MIR2682 100616452 microRNA 2682 491 211958_at IGFBP5 3488 insulin like growth factor ... 492 209589_s_at EPHB2 2048 EPH receptor B2 493 227808_at DNAJC15 29103 DnaJ heat shock protein fam... 494 228948_at EPHA4 2043 EPH receptor A4 495 236369_at <NA> <NA> <NA> 496 205872_x_at PDE4DIP 9659 phosphodiesterase 4D intera... 497 236523_at C4orf54 285556 chromosome 4 open reading f... 498 223878_at INPP4B 8821 inositol polyphosphate-4-ph... 499 219855_at NUDT11 55190 nudix hydrolase 11 500 212419_at ZCCHC24 219654 zinc finger CCHC-type conta... 501 236798_at LINC00888 100505687 long intergenic non-protein... 502 229842_at ELF3 1999 E74 like ETS transcription ... 503 213156_at ZBTB20 26137 zinc finger and BTB domain ... 504 207069_s_at SMAD6 4091 SMAD family member 6 505 209723_at SERPINB9 5272 serpin family B member 9 506 207818_s_at HTR7 3363 5-hydroxytryptamine receptor 7 507 1558048_x_at <NA> <NA> <NA> 508 231993_at ITGBL1 9358 integrin subunit beta like 1 509 206828_at TXK 7294 TXK tyrosine kinase 510 206876_at SIM1 6492 SIM bHLH transcription fact... 511 236281_x_at HTR7 3363 5-hydroxytryptamine receptor 7 512 213325_at NECTIN3 25945 nectin cell adhesion molecu... 513 222773_s_at GALNT12 79695 polypeptide N-acetylgalacto... 514 242396_at NR2F2 7026 nuclear receptor subfamily ... 515 210612_s_at SYNJ2 8871 synaptojanin 2 516 213712_at ELOVL2 54898 ELOVL fatty acid elongase 2 517 229372_at GOLT1A 127845 golgi transport 1A 518 231248_at CST6 1474 cystatin E/M 519 216098_s_at HTR7P1 93164 5-hydroxytryptamine recepto... 520 216098_s_at HTR7 3363 5-hydroxytryptamine receptor 7 521 226592_at ZNF618 114991 zinc finger protein 618 522 213807_x_at MET 4233 MET proto-oncogene, recepto... 523 229464_at MYEF2 50804 myelin expression factor 2 524 228481_at <NA> <NA> <NA> 525 1557050_at <NA> <NA> <NA> 526 1554333_at DNAJA4 55466 DnaJ heat shock protein fam... 527 219850_s_at EHF 26298 ETS homologous factor 528 214927_at ITGBL1 9358 integrin subunit beta like 1 529 235236_at INSYN2B 100131897 inhibitory synaptic factor ... 530 204035_at SCG2 7857 secretogranin II 531 230183_at EXT1 2131 exostosin glycosyltransfera... 532 222168_at <NA> <NA> <NA> 533 214500_at MACROH2A1 9555 macroH2A.1 histone 534 209119_x_at NR2F2 7026 nuclear receptor subfamily ... 535 240407_at NAV2-AS6 100126784 NAV2 antisense RNA 6 536 205421_at SLC22A3 6581 solute carrier family 22 me... 537 235122_at HIVEP3 59269 HIVEP zinc finger 3 538 212095_s_at MTUS1 57509 microtubule associated scaf... 539 209905_at HOXA9 3205 homeobox A9 540 209905_at HOXA10-HOXA9 100534589 HOXA10-HOXA9 readthrough 541 205466_s_at HS3ST1 9957 heparan sulfate-glucosamine... 542 236917_at LRRC34 151827 leucine rich repeat contain... 543 225355_at NEURL1B 54492 neuralized E3 ubiquitin pro... 544 224989_at SMIM14 201895 small integral membrane pro... 545 223217_s_at NFKBIZ 64332 NFKB inhibitor zeta 546 223226_x_at SSBP4 170463 single stranded DNA binding... 547 230329_s_at NUDT6 11162 nudix hydrolase 6 548 235643_at SAMD9L 219285 sterile alpha motif domain ... 549 1557080_s_at ITGBL1 9358 integrin subunit beta like 1 550 230831_at FRMD5 84978 FERM domain containing 5 551 206805_at SEMA3A 10371 semaphorin 3A 552 208711_s_at CCND1 595 cyclin D1 553 210875_s_at ZEB1 6935 zinc finger E-box binding h... 554 229435_at GLIS3 169792 GLIS family zinc finger 3 555 206941_x_at SEMA3E 9723 semaphorin 3E 556 1559361_at MACC1 346389 MET transcriptional regulat... 557 1559361_at LOC101927668 101927668 uncharacterized LOC101927668 558 219451_at MSRB2 22921 methionine sulfoxide reduct... 559 1557236_at APOL6 80830 apolipoprotein L6 560 1552309_a_at NEXN 91624 nexilin F-actin binding pro... 561 224920_x_at MYADM 91663 myeloid associated differen... 562 225575_at LIFR 3977 LIF receptor subunit alpha 563 236029_at FAT3 120114 FAT atypical cadherin 3 564 206330_s_at SHC3 53358 SHC adaptor protein 3 565 206290_s_at RGS7 6000 regulator of G protein sign... 566 236489_at ADGRF1 266977 adhesion G protein-coupled ... 567 209750_at NR1D2 9975 nuclear receptor subfamily ... 568 235331_x_at PCGF5 84333 polycomb group ring finger 5 569 224822_at DLC1 10395 DLC1 Rho GTPase activating ... 570 244852_at DSEL 92126 dermatan sulfate epimerase ... 571 222932_at EHF 26298 ETS homologous factor 572 213590_at SLC16A5 9121 solute carrier family 16 me... 573 227053_at PACSIN1 29993 protein kinase C and casein... 574 214647_s_at HFE 3077 homeostatic iron regulator 575 242629_at RAB3B 5865 RAB3B, member RAS oncogene ... 576 230036_at SAMD9L 219285 sterile alpha motif domain ... 577 235030_at NXPE3 91775 neurexophilin and PC-estera... 578 201867_s_at TBL1X 6907 transducin beta like 1 X-li... 579 204749_at NAP1L3 4675 nucleosome assembly protein... 580 213816_s_at MET 4233 MET proto-oncogene, recepto... 581 235563_at GPRC5A 9052 G protein-coupled receptor ... 582 230003_at SLC16A7 9194 solute carrier family 16 me... 583 229963_at BEX5 340542 brain expressed X-linked 5 584 206084_at PTPRR 5801 protein tyrosine phosphatas... 585 210173_at PTPRJ 5795 protein tyrosine phosphatas... 586 228697_at HINT3 135114 histidine triad nucleotide ... 587 238520_at TRERF1 55809 transcriptional regulating ... 588 207029_at KITLG 4254 KIT ligand 589 215506_s_at DIRAS3 9077 DIRAS family GTPase 3 590 211020_at GCNT2 2651 glucosaminyl (N-acetyl) tra... 591 219557_s_at NRIP3 56675 nuclear receptor interactin... 592 203355_s_at PSD3 23362 pleckstrin and Sec7 domain ... 593 224496_s_at TMEM107 84314 transmembrane protein 107 594 1555229_a_at C1S 716 complement C1s 595 226533_at HINT3 135114 histidine triad nucleotide ... 596 211124_s_at KITLG 4254 KIT ligand 597 242134_at <NA> <NA> <NA>
Key Points
BioConductor has a rich annotation infrastructure, with different data type being stored in different annotation packages.
The
select()function allows us to efficiently query annotation databases.Using
topTable()in conjunction withrownames()allows us to retrieve all the probes which are differentially expressed between our experimental conditions.