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Table 2 Annotation counts from 2013 to 2016

From: Sensing the cilium, digital capture of ciliary data for comparative genomics investigations

Curation status GO term category Experimental Unknown Curator statement Author statement Sequence Phylogenetic Electronic Total
A. Annotation counts in July 2013
 Completed genes (134) Ciliary 153 0 5 79 0 41 278
Related 225 0 3 92 0 16 336
Other 316 87 0 18 328 0 598 1347
 Not yet targeted genes (176) Ciliary 196 3 0 74 1 18 292
Related 705 0 6 168 12 22 913
Other 1867 91 2 56 1192 49 934 4191
  Total 3462 178 5 88 1933 62 1629 7357
B. Annotation counts in December 2016
 Completed genes (134) Ciliary 504 21 1 214 45 37 822
Related 511 0 3 149 17 17 697
Other 689 41 3 7 525 81 618 1964
 Not yet targeted genes (176) Ciliary 317 4 0 158 20 18 517
Related 830 0 6 214 29 25 1104
Other 2344 54 4 65 1712 216 905 5300
  Total 5195 95 32 82 2972 408 1620 10,404
C. Difference in annotation counts from 2013 to 2016
 Completed genes (134) Ciliary 351 21 − 4 135 45 − 4 544
Related 286 0 0 57 17 1 361
Other 373 − 46 3 − 11 197 81 20 617
 Not yet targeted genes (176) Ciliary 121 1 0 84 19 0 225
Related 125 0 0 46 17 3 191
Other 477 − 37 2 9 520 167 − 29 1109
  Total 1733 − 83 27 − 6 1039 346 − 9 3047
D. Fold change in annotations from 2013 to 2016
 Completed genes (134) Ciliary 3.29 DZ 0.20 2.71 DZ 0.90 2.96
Related 2.27 DZ 1.00 1.62 DZ 1.06 2.07
Other 2.18 0.47 DZ 0.39 1.60 DZ 1.03 1.46
 Not yet targeted genes (176) Ciliary 1.62 1.33 DZ 2.14 20.00 1.00 1.77
Related 1.18 DZ 1.00 1.27 2.42 1.14 1.21
Other 1.26 0.59 2.00 1.16 1.44 4.41 0.97 1.26
  Total 1.50 0.53 6.40 0.93 1.54 6.58 0.99 1.41
  1. These tables show the number of annotations (excluding annotations with the NOT qualifier) by evidence type for the 310 mouse ciliary genes corresponding to the SYSCILIA Gold Standard set of human ciliary genes before our annotation project commenced in July 2013 (Panel A) and as of December 2016 (Panel B). The difference in the number of annotations from July 2013 to December 2016 is shown in Panel C and the fold difference in Panel D. “Completed genes” are those which have been annotated as fully as possible as of December 2016, while “genes not yet targeted” are those which have not yet been focused on specifically for comprehensive curation. However, some of these genes have received additional annotations during the project, generally due to being present in the same references as genes which were targeted for curation. GO annotations are categorized by type of evidence code. “Experimental” includes these evidence codes: IDA, IMP, IGI, IPI, and IEP. “Unknown” refers to annotations to the root node of each of the three aspects of GO using the ND evidence code indicating that nothing is known. As the three root terms are not part of either the ciliary or related term sets, a dash indicates that it is not possible to have unknown annotations in these categories. “Author statement” evidence includes both TAS and NAS codes. “Curator statement” refers to annotations using the evidence code IC. “Sequence” includes ISO, ISA, ISS, and ISM. “Phylogenetic” includes annotations made with the evidence code In IBA using the PAINT tool for phylogenetic annotation. “Electronic” refers to annotations made with the Inferred from IEA code, for example, annotations made on the basis of the presence of a specific InterPRO domain. For more information and expansions of the evidence code acronyms, see Additional file 4. The presence of DZ in a cell in part D indicates that there were zero annotations in 2013, making it impossible to calculate fold change