Skip to main content

Table 2 Gene Ontology annotation for 90e set sequences.

From: Smed454 dataset: unravelling the transcriptome of Schmidtea mediterranea

GO Molecular Function Count Freq% GO Biological Process Count Freq% GO Cellular Component Count Freq%
GO:0000166 nucleotide binding 54,823 --- --- --- --- --- GO:0043229 intracellular organelle 60,817 ---
--- unannotated 9,709 --- --- unannotated 62,834 --- --- unannotated 11,131 ---
GO:0016787 hydrolase activity 5,197 35.669 GO:0043170 macromolecule metabolic process 5,793 35.610 GO:0043234 protein complex 2,918 40.788
GO:0016740 transferase activity 2,030 13.933 GO:0022607 cellular component assembly 2,182 13.413 GO:0044424 intracellular part 2,314 32.346
GO:0043167 ion binding 1,323 9.080 GO:0006810 transport 1,213 7.456 GO:0031982 vesicle 819 11.448
GO:0003735 structural constituent of ribosome 874 5.999 GO:0006950 response to stress 1,070 6.577 GO:0044425 membrane part 469 6.556
GO:0005488 binding 761 5.223 GO:0050789 regulation of biological process 1,012 6.221 GO:0016020 membrane 210 2.935
GO:0016491 oxidoreductase activity 703 4.825 GO:0006807 nitrogen compound metabolic process 722 4.438 GO:0005622 intracellular 111 1.552
GO:0022857 transmembrane transporter activity 678 4.653 GO:0048869 cellular developmental process 655 4.026 GO:0044446 intracellular organelle part 91 1.272
GO:0030235 nitric-oxide synthase regulator activity 597 4.097 GO:0065009 regulation of molecular function 622 3.823 GO:0005576 extracellular region 63 0.881
GO:0043176 amine binding 580 3.981 GO:0009056 catabolic process 507 3.117 GO:0045211 postsynaptic membrane 21 0.294
GO:0005515 protein binding 532 3.651 GO:0044419 interspecies interaction between organisms 280 1.721 GO:0044420 extracellular matrix part 19 0.266
GO:0003676 nucleic acid binding 401 2.752 GO:0055114 oxidation reduction 236 1.451 GO:0043233 organelle lumen 18 0.252
GO:0005215 transporter activity 387 2.656 GO:0065008 regulation of biological quality 206 1.266 GO:0031012 extracellular matrix 16 0.224
GO:0016829 lyase activity 71 0.487 GO:0048856 anatomical structure development 193 1.186 GO:0042597 periplasmic space 15 0.210
GO:0016853 isomerase activity 55 0.377 GO:0051649 establishment of localization in cell 183 1.125 GO:0000267 cell fraction 15 0.210
GO:0048037 cofactor binding 52 0.357 GO:0044237 cellular metabolic process 182 1.119 GO:0044462 external encapsulating structure part 11 0.154
GO:0016874 ligase activity 49 0.336 GO:0023060 signal transmission 150 0.922 GO:0031975 envelope 8 0.112
GO:0004871 signal transducer activity 45 0.309 GO:0048870 cell motility 141 0.867 GO:0005615 extracellular space 7 0.098
GO:0003824 catalytic activity 32 0.220 GO:0008152 metabolic process 139 0.854 GO:0009986 cell surface 6 0.084
GO:0060589 nucleoside-triphosphatase regulator activity 32 0.220 GO:0023033 signaling pathway 107 0.658 GO:0043204 perikaryon 5 0.070
GO:0042277 peptide binding 28 0.192 GO:0044238 primary metabolic process 83 0.510 GO:0030427 site of polarized growth 4 0.056
GO:0022892 substrate-specific transporter activity 22 0.151 GO:0042221 response to chemical stimulus 69 0.424 GO:0042995 cell projection 3 0.042
GO:0019208 phosphatase regulator activity 12 0.082 GO:0006996 organelle organization 47 0.289 GO:0030312 external encapsulating structure 2 0.028
GO:0003712 transcription cofactor activity 12 0.082 GO:0007017 microtubule-based process 42 0.258 GO:0031594 neuromuscular junction 2 0.028
GO:0019207 kinase regulator activity 11 0.075 GO:0044281 small molecule metabolic process 39 0.240 GO:0045177 apical part of cell 2 0.028
GO:0008289 lipid binding 9 0.062 GO:0051301 cell division 37 0.227 GO:0019028 viral capsid 1 0.014
GO:0005201 extracellular matrix structural constituent 8 0.055 GO:0022613 ribonucleoprotein complex biogenesis 35 0.215 GO:0031252 cell leading edge 1 0.014
GO:0050840 extracellular matrix binding 6 0.041 GO:0019637 organophosphate metabolic process 34 0.209 GO:0044217 other organism part 1 0.014
GO:0061134 peptidase regulator activity 6 0.041 GO:0045184 establishment of protein localization 34 0.209 GO:0044297 cell body 1 0.014
GO:0030246 carbohydrate binding 6 0.041 GO:0009628 response to abiotic stimulus 23 0.141 GO:0044463 cell projection part 1 0.014
GO:0016248 channel inhibitor activity 5 0.034 GO:0019748 secondary metabolic process 21 0.129   TOTAL 7,154  
GO:0003702 RNA polymerase II transcription factor activity 5 0.034 GO:0009058 biosynthetic process 21 0.129     
GO:0005198 structural molecule activity 4 0.027 GO:0007155 cell adhesion 18 0.111     
GO:0016986 transcription initiation factor activity 4 0.027 GO:0061024 membrane organization 16 0.098     
GO:0042165 neurotransmitter binding 4 0.027 GO:0007275 multicellular organismal development 16 0.098     
GO:0003682 chromatin binding 3 0.021 GO:0016192 vesicle-mediated transport 12 0.074     
GO:0008430 selenium binding 3 0.021 GO:0043062 extracellular structure organization 10 0.061     
GO:0030234 enzyme regulator activity 2 0.014 GO:0034330 cell junction organization 9 0.055     
GO:0030528 transcription regulator activity 2 0.014 GO:0048609 reproductive process in a multicellular organism 9 0.055     
GO:0009055 electron carrier activity 2 0.014 GO:0007154 cell communication 8 0.049     
GO:0017056 structural constituent of nuclear pore 2 0.014 GO:0003008 system process 7 0.043     
GO:0017080 sodium channel regulator activity 2 0.014 GO:0016049 cell growth 7 0.043     
GO:0001871 pattern binding 2 0.014 GO:0016458 gene silencing 6 0.037     
GO:0019239 deaminase activity 2 0.014 GO:0008219 cell death 5 0.031     
GO:0043021 ribonucleoprotein binding 2 0.014 GO:0033036 macromolecule localization 4 0.025     
GO:0008538 proteasome activator activity 2 0.014 GO:0048610 reproductive cellular process 4 0.025     
GO:0030337 DNA polymerase processivity factor activity 1 0.007 GO:0051236 establishment of RNA localization 4 0.025     
GO:0031406 carboxylic acid binding 1 0.007 GO:0071684 organism emergence from protective structure 4 0.025     
GO:0042562 hormone binding 1 0.007 GO:0006955 immune response 4 0.025     
GO:0046906 tetrapyrrole binding 1 0.007 GO:0007049 cell cycle 4 0.025     
GO:0051540 metal cluster binding 1 0.007 GO:0009405 pathogenesis 4 0.025     
  TOTAL 14,570   GO:0009607 response to biotic stimulus 4 0.025     
     GO:0009791 post-embryonic development 4 0.025     
     GO:0048646 anatomical structure formation involved in morphogenesis 4 0.025     
     GO:0009790 embryonic development 3 0.018     
     GO:0015976 carbon utilization 2 0.012     
     GO:0032506 cytokinetic process 2 0.012     
     GO:0045103 intermediate filament-based process 2 0.012     
     GO:0070882 cellular cell wall organization or biogenesis 2 0.012     
     GO:0006413 translational initiation 2 0.012     
     GO:0009566 fertilization 2 0.012     
     GO:0001906 cell killing 1 0.006     
     GO:0043473 pigmentation 1 0.006     
     GO:0009987 cellular process 1 0.006     
     GO:0022402 cell cycle process 1 0.006     
     GO:0022411 cellular component disassembly 1 0.006     
     GO:0022415 viral reproductive process 1 0.006     
     GO:0023061 signal release 1 0.006     
     GO:0030030 cell projection organization 1 0.006     
     GO:0051606 detection of stimulus 1 0.006     
     GO:0000746 conjugation 1 0.006     
     GO:0007163 establishment or maintenance of cell polarity 1 0.006     
     GO:0009653 anatomical structure morphogenesis 1 0.006     
      TOTAL 16,268      
  1. The most probable GO code in the three ontology categories--molecular function, biological process and cellular component-- for each sequence in the 90e data set was selected. For simplicity, only level one and two codes are shown here in order.