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PMC:1186732 / 53515-54676 JSONTXT

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craft-sa-dev

Id Subject Object Predicate Lexical cue
T12091 0-3 CD denotes Two
T12092 4-9 NNS denotes types
T12093 32-41 VBN denotes performed
T12094 10-12 IN denotes of
T12095 13-26 NN denotes normalization
T12096 27-31 VBD denotes were
T12097 42-44 IN denotes on
T12098 45-48 DT denotes the
T12099 63-69 NNS denotes scores
T12100 49-52 JJ denotes raw
T12101 53-62 NN denotes intensity
T12102 70-77 VBN denotes derived
T12103 78-82 IN denotes from
T12104 83-86 DT denotes the
T12105 99-107 NN denotes analysis
T12106 87-94 NNP denotes GenePix
T12107 95-98 NNP denotes Pro
T12108 107-108 . denotes .
T12109 108-274 sentence denotes First, for a given experiment, the average intensity of all the spots in the weaker of the two channels (Cy3 or Cy5) was normalized to those in the stronger channel.
T12110 109-114 RB denotes First
T12111 230-240 VBN denotes normalized
T12112 114-116 , denotes ,
T12113 116-119 IN denotes for
T12114 120-121 DT denotes a
T12115 128-138 NN denotes experiment
T12116 122-127 VBN denotes given
T12117 138-140 , denotes ,
T12118 140-143 DT denotes the
T12119 152-161 NN denotes intensity
T12120 144-151 JJ denotes average
T12121 162-164 IN denotes of
T12122 165-168 PDT denotes all
T12123 173-178 NNS denotes spots
T12124 169-172 DT denotes the
T12125 179-181 IN denotes in
T12126 182-185 DT denotes the
T12127 186-192 JJR denotes weaker
T12128 193-195 IN denotes of
T12129 196-199 DT denotes the
T12130 204-212 NNS denotes channels
T12131 200-203 CD denotes two
T12132 213-214 -LRB- denotes (
T12133 214-217 NN denotes Cy3
T12134 218-220 CC denotes or
T12135 221-224 NN denotes Cy5
T12136 224-225 -RRB- denotes )
T12137 226-229 VBD denotes was
T12138 241-243 IN denotes to
T12139 244-249 DT denotes those
T12140 250-252 IN denotes in
T12141 253-256 DT denotes the
T12142 266-273 NN denotes channel
T12143 257-265 JJR denotes stronger
T12144 273-274 . denotes .
T12145 274-529 sentence denotes Second, in a given set of experiments done in triplicate at a particular time point, the two experiments with the weaker average signal intensity over all spots were normalized to those in the third microarray with the strongest average signal intensity.
T12146 275-281 RB denotes Second
T12147 441-451 VBN denotes normalized
T12148 281-283 , denotes ,
T12149 283-285 IN denotes in
T12150 286-287 DT denotes a
T12151 294-297 NN denotes set
T12152 288-293 VBN denotes given
T12153 298-300 IN denotes of
T12154 301-312 NNS denotes experiments
T12155 313-317 VBN denotes done
T12156 318-320 IN denotes in
T12157 321-331 NN denotes triplicate
T12158 332-334 IN denotes at
T12159 335-336 DT denotes a
T12160 353-358 NN denotes point
T12161 337-347 JJ denotes particular
T12162 348-352 NN denotes time
T12163 358-360 , denotes ,
T12164 360-363 DT denotes the
T12165 368-379 NNS denotes experiments
T12166 364-367 CD denotes two
T12167 380-384 IN denotes with
T12168 385-388 DT denotes the
T12169 411-420 NN denotes intensity
T12170 389-395 JJR denotes weaker
T12171 396-403 JJ denotes average
T12172 404-410 NN denotes signal
T12173 421-425 IN denotes over
T12174 426-429 DT denotes all
T12175 430-435 NNS denotes spots
T12176 436-440 VBD denotes were
T12177 452-454 IN denotes to
T12178 455-460 DT denotes those
T12179 461-463 IN denotes in
T12180 464-467 DT denotes the
T12181 474-484 NN denotes microarray
T12182 468-473 JJ denotes third
T12183 485-489 IN denotes with
T12184 490-493 DT denotes the
T12185 519-528 NN denotes intensity
T12186 494-503 JJS denotes strongest
T12187 504-511 JJ denotes average
T12188 512-518 NN denotes signal
T12189 528-529 . denotes .
T12190 529-619 sentence denotes All spots with signal levels equal to or below background were removed from the analysis.
T12191 530-533 DT denotes All
T12192 534-539 NNS denotes spots
T12193 593-600 VBN denotes removed
T12194 540-544 IN denotes with
T12195 545-551 NN denotes signal
T12196 552-558 NNS denotes levels
T12197 559-564 JJ denotes equal
T12198 565-567 IN denotes to
T12199 568-570 CC denotes or
T12200 571-576 IN denotes below
T12201 577-587 NN denotes background
T12202 588-592 VBD denotes were
T12203 601-605 IN denotes from
T12204 606-609 DT denotes the
T12205 610-618 NN denotes analysis
T12206 618-619 . denotes .
T12207 619-679 sentence denotes The resulting files contained on average about 6,000 spots.
T12208 620-623 DT denotes The
T12209 634-639 NNS denotes files
T12210 624-633 VBG denotes resulting
T12211 640-649 VBD denotes contained
T12212 650-652 IN denotes on
T12213 653-660 JJ denotes average
T12215 667-672 CD denotes 6,000
T12216 673-678 NNS denotes spots
T12217 678-679 . denotes .
T12218 679-979 sentence denotes These files were then sorted according to Cy3/Cy5 signal intensity, and those spots with the 10% highest and 10% lowest intensity ratios (approximately 600 spots/experiment) were compared across the three experiments at a given time point using custom Perl scripts (available upon request from JCC).
T12219 680-685 DT denotes These
T12220 686-691 NNS denotes files
T12221 702-708 VBN denotes sorted
T12222 692-696 VBD denotes were
T12223 697-701 RB denotes then
T12224 709-718 VBG denotes according
T12225 719-721 IN denotes to
T12226 722-725 NN denotes Cy3
T12227 726-729 NN denotes Cy5
T12228 725-726 HYPH denotes /
T12229 737-746 NN denotes intensity
T12230 730-736 NN denotes signal
T12231 746-748 , denotes ,
T12232 748-751 CC denotes and
T12233 752-757 DT denotes those
T12234 758-763 NNS denotes spots
T12235 859-867 VBN denotes compared
T12236 764-768 IN denotes with
T12237 769-772 DT denotes the
T12238 810-816 NNS denotes ratios
T12239 773-775 CD denotes 10
T12240 775-776 NN denotes %
T12241 777-784 JJS denotes highest
T12242 785-788 CC denotes and
T12243 789-791 CD denotes 10
T12244 791-792 NN denotes %
T12245 793-799 JJS denotes lowest
T12246 800-809 NN denotes intensity
T12247 817-818 -LRB- denotes (
T12248 836-841 NNS denotes spots
T12249 818-831 RB denotes approximately
T12250 832-835 CD denotes 600
T12251 841-842 SYM denotes /
T12253 852-853 -RRB- denotes )
T12254 854-858 VBD denotes were
T12255 868-874 IN denotes across
T12256 875-878 DT denotes the
T12257 885-896 NNS denotes experiments
T12258 879-884 CD denotes three
T12259 897-899 IN denotes at
T12260 900-901 DT denotes a
T12261 913-918 NN denotes point
T12262 902-907 VBN denotes given
T12263 908-912 NN denotes time
T12264 919-924 VBG denotes using
T12265 925-931 NN denotes custom
T12266 937-944 NNS denotes scripts
T12267 932-936 NN denotes Perl
T12268 945-946 -LRB- denotes (
T12269 946-955 JJ denotes available
T12270 956-960 IN denotes upon
T12271 961-968 NN denotes request
T12272 969-973 IN denotes from
T12273 974-977 NNP denotes JCC
T12274 977-978 -RRB- denotes )
T12275 978-979 . denotes .
T12276 979-1161 sentence denotes All spots which were present in the top 10% most up- or down-regulated genes in two out of three or three out of three experiments were recorded (the latter are listed in Table S3).
T12277 980-983 DT denotes All
T12278 984-989 NNS denotes spots
T12279 1116-1124 VBN denotes recorded
T12280 990-995 WDT denotes which
T12281 996-1000 VBD denotes were
T12282 1001-1008 JJ denotes present
T12283 1009-1011 IN denotes in
T12284 1012-1015 DT denotes the
T12285 1022-1023 NN denotes %
T12286 1016-1019 JJ denotes top
T12287 1020-1022 CD denotes 10
T12288 1051-1056 NNS denotes genes
T12289 1024-1028 RBS denotes most
T12290 1041-1050 VBN denotes regulated
T12291 1029-1031 RB denotes up
T12292 1031-1032 HYPH denotes -
T12293 1033-1035 CC denotes or
T12294 1036-1040 RB denotes down
T12295 1040-1041 HYPH denotes -
T12296 1057-1059 IN denotes in
T12297 1060-1063 CD denotes two
T12298 1071-1076 CD denotes three
T12299 1064-1067 IN denotes out
T12300 1068-1070 IN denotes of
T12301 1099-1110 NNS denotes experiments
T12302 1077-1079 CC denotes or
T12303 1080-1085 CD denotes three
T12304 1093-1098 CD denotes three
T12305 1086-1089 IN denotes out
T12306 1090-1092 IN denotes of
T12307 1111-1115 VBD denotes were
T12308 1125-1126 -LRB- denotes (
T12309 1141-1147 VBN denotes listed
T12310 1126-1129 DT denotes the
T12311 1130-1136 JJ denotes latter
T12312 1137-1140 VBP denotes are
T12313 1148-1150 IN denotes in
T12314 1151-1156 NN denotes Table
T12315 1157-1159 NN denotes S3
T12316 1159-1160 -RRB- denotes )
T12317 1160-1161 . denotes .
T12214 661-666 IN denotes about
T12252 842-852 NN denotes experiment
R8038 T12091 T12092 nummod Two,types
R8039 T12092 T12093 nsubjpass types,performed
R8040 T12094 T12092 prep of,types
R8041 T12095 T12094 pobj normalization,of
R8042 T12096 T12093 auxpass were,performed
R8043 T12097 T12093 prep on,performed
R8044 T12098 T12099 det the,scores
R8045 T12099 T12097 pobj scores,on
R8046 T12100 T12099 amod raw,scores
R8047 T12101 T12099 compound intensity,scores
R8048 T12102 T12099 acl derived,scores
R8049 T12103 T12102 prep from,derived
R8050 T12104 T12105 det the,analysis
R8051 T12105 T12103 pobj analysis,from
R8052 T12106 T12107 compound GenePix,Pro
R8053 T12107 T12105 compound Pro,analysis
R8054 T12108 T12093 punct .,performed
R8055 T12110 T12111 advmod First,normalized
R8056 T12112 T12111 punct ", ",normalized
R8057 T12113 T12111 prep for,normalized
R8058 T12114 T12115 det a,experiment
R8059 T12115 T12113 pobj experiment,for
R8060 T12116 T12115 amod given,experiment
R8061 T12117 T12111 punct ", ",normalized
R8062 T12118 T12119 det the,intensity
R8063 T12119 T12111 nsubjpass intensity,normalized
R8064 T12120 T12119 amod average,intensity
R8065 T12121 T12119 prep of,intensity
R8066 T12122 T12123 predet all,spots
R8067 T12123 T12121 pobj spots,of
R8068 T12124 T12123 det the,spots
R8069 T12125 T12123 prep in,spots
R8070 T12126 T12127 det the,weaker
R8071 T12127 T12125 pobj weaker,in
R8072 T12128 T12127 prep of,weaker
R8073 T12129 T12130 det the,channels
R8074 T12130 T12128 pobj channels,of
R8075 T12131 T12130 nummod two,channels
R8076 T12132 T12133 punct (,Cy3
R8077 T12133 T12130 parataxis Cy3,channels
R8078 T12134 T12133 cc or,Cy3
R8079 T12135 T12133 conj Cy5,Cy3
R8080 T12136 T12133 punct ),Cy3
R8081 T12137 T12111 auxpass was,normalized
R8082 T12138 T12111 prep to,normalized
R8083 T12139 T12138 pobj those,to
R8084 T12140 T12139 prep in,those
R8085 T12141 T12142 det the,channel
R8086 T12142 T12140 pobj channel,in
R8087 T12143 T12142 amod stronger,channel
R8088 T12144 T12111 punct .,normalized
R8089 T12146 T12147 advmod Second,normalized
R8090 T12148 T12147 punct ", ",normalized
R8091 T12149 T12147 prep in,normalized
R8092 T12150 T12151 det a,set
R8093 T12151 T12149 pobj set,in
R8094 T12152 T12151 amod given,set
R8095 T12153 T12151 prep of,set
R8096 T12154 T12153 pobj experiments,of
R8097 T12155 T12154 acl done,experiments
R8098 T12156 T12155 prep in,done
R8099 T12157 T12156 pobj triplicate,in
R8100 T12158 T12155 prep at,done
R8101 T12159 T12160 det a,point
R8102 T12160 T12158 pobj point,at
R8103 T12161 T12160 amod particular,point
R8104 T12162 T12160 compound time,point
R8105 T12163 T12147 punct ", ",normalized
R8106 T12164 T12165 det the,experiments
R8107 T12165 T12147 nsubjpass experiments,normalized
R8108 T12166 T12165 nummod two,experiments
R8109 T12167 T12165 prep with,experiments
R8110 T12168 T12169 det the,intensity
R8111 T12169 T12167 pobj intensity,with
R8112 T12170 T12169 amod weaker,intensity
R8113 T12171 T12169 amod average,intensity
R8114 T12172 T12169 compound signal,intensity
R8115 T12173 T12169 prep over,intensity
R8116 T12174 T12175 det all,spots
R8117 T12175 T12173 pobj spots,over
R8118 T12176 T12147 auxpass were,normalized
R8119 T12177 T12147 prep to,normalized
R8120 T12178 T12177 pobj those,to
R8121 T12179 T12178 prep in,those
R8122 T12180 T12181 det the,microarray
R8123 T12181 T12179 pobj microarray,in
R8124 T12182 T12181 amod third,microarray
R8125 T12183 T12178 prep with,those
R8126 T12184 T12185 det the,intensity
R8127 T12185 T12183 pobj intensity,with
R8128 T12186 T12185 amod strongest,intensity
R8129 T12187 T12185 amod average,intensity
R8130 T12188 T12185 compound signal,intensity
R8131 T12189 T12147 punct .,normalized
R8132 T12191 T12192 det All,spots
R8133 T12192 T12193 nsubjpass spots,removed
R8134 T12194 T12192 prep with,spots
R8135 T12195 T12196 compound signal,levels
R8136 T12196 T12194 pobj levels,with
R8137 T12197 T12196 amod equal,levels
R8138 T12198 T12197 prep to,equal
R8139 T12199 T12197 cc or,equal
R8140 T12200 T12201 prep below,background
R8141 T12201 T12197 conj background,equal
R8142 T12202 T12193 auxpass were,removed
R8143 T12203 T12193 prep from,removed
R8144 T12204 T12205 det the,analysis
R8145 T12205 T12203 pobj analysis,from
R8146 T12206 T12193 punct .,removed
R8147 T12208 T12209 det The,files
R8148 T12209 T12211 nsubj files,contained
R8149 T12210 T12209 amod resulting,files
R8150 T12212 T12211 prep on,contained
R8151 T12213 T12212 amod average,on
R8152 T12214 T12215 quantmod about,"6,000"
R8153 T12215 T12216 nummod "6,000",spots
R8154 T12216 T12211 dobj spots,contained
R8155 T12217 T12211 punct .,contained
R8156 T12219 T12220 det These,files
R8157 T12220 T12221 nsubjpass files,sorted
R8158 T12222 T12221 auxpass were,sorted
R8159 T12223 T12221 advmod then,sorted
R8160 T12224 T12221 prep according,sorted
R8161 T12225 T12224 prep to,according
R8162 T12226 T12227 compound Cy3,Cy5
R8163 T12227 T12229 compound Cy5,intensity
R8164 T12228 T12227 punct /,Cy5
R8165 T12229 T12225 pobj intensity,to
R8166 T12230 T12229 compound signal,intensity
R8167 T12231 T12221 punct ", ",sorted
R8168 T12232 T12221 cc and,sorted
R8169 T12233 T12234 det those,spots
R8170 T12234 T12235 nsubjpass spots,compared
R8171 T12235 T12221 conj compared,sorted
R8172 T12236 T12234 prep with,spots
R8173 T12237 T12238 det the,ratios
R8174 T12238 T12236 pobj ratios,with
R8175 T12239 T12240 nummod 10,%
R8176 T12240 T12241 npadvmod %,highest
R8177 T12241 T12238 amod highest,ratios
R8178 T12242 T12241 cc and,highest
R8179 T12243 T12244 nummod 10,%
R8180 T12244 T12245 npadvmod %,lowest
R8181 T12245 T12241 conj lowest,highest
R8182 T12246 T12238 compound intensity,ratios
R8183 T12247 T12248 punct (,spots
R8184 T12248 T12234 parataxis spots,spots
R8185 T12249 T12250 advmod approximately,600
R8186 T12250 T12248 nummod 600,spots
R8187 T12251 T12252 punct /,experiment
R8188 T12252 T12248 prep experiment,spots
R8189 T12253 T12248 punct ),spots
R8190 T12254 T12235 auxpass were,compared
R8191 T12255 T12235 prep across,compared
R8192 T12256 T12257 det the,experiments
R8193 T12257 T12255 pobj experiments,across
R8194 T12258 T12257 nummod three,experiments
R8195 T12259 T12235 prep at,compared
R8196 T12260 T12261 det a,point
R8197 T12261 T12259 pobj point,at
R8198 T12262 T12261 amod given,point
R8199 T12263 T12261 compound time,point
R8200 T12264 T12235 advcl using,compared
R8201 T12265 T12266 compound custom,scripts
R8202 T12266 T12264 dobj scripts,using
R8203 T12267 T12266 compound Perl,scripts
R8204 T12268 T12266 punct (,scripts
R8205 T12269 T12266 relcl available,scripts
R8206 T12270 T12269 prep upon,available
R8207 T12271 T12270 pobj request,upon
R8208 T12272 T12269 prep from,available
R8209 T12273 T12272 pobj JCC,from
R8210 T12274 T12235 punct ),compared
R8211 T12275 T12235 punct .,compared
R8212 T12277 T12278 det All,spots
R8213 T12278 T12279 nsubjpass spots,recorded
R8214 T12280 T12281 dep which,were
R8215 T12281 T12278 relcl were,spots
R8216 T12282 T12281 acomp present,were
R8217 T12283 T12281 prep in,were
R8218 T12284 T12285 det the,%
R8219 T12285 T12288 nmod %,genes
R8220 T12286 T12285 amod top,%
R8221 T12287 T12285 nummod 10,%
R8222 T12288 T12283 pobj genes,in
R8223 T12289 T12290 advmod most,regulated
R8224 T12290 T12288 amod regulated,genes
R8225 T12291 T12290 advmod up,regulated
R8226 T12292 T12291 punct -,up
R8227 T12293 T12291 cc or,up
R8228 T12294 T12291 conj down,up
R8229 T12295 T12290 punct -,regulated
R8230 T12296 T12281 prep in,were
R8231 T12297 T12298 quantmod two,three
R8232 T12298 T12301 nummod three,experiments
R8233 T12299 T12298 quantmod out,three
R8234 T12300 T12298 quantmod of,three
R8235 T12301 T12296 pobj experiments,in
R8236 T12302 T12298 cc or,three
R8237 T12303 T12304 quantmod three,three
R8238 T12304 T12298 conj three,three
R8239 T12305 T12304 quantmod out,three
R8240 T12306 T12304 quantmod of,three
R8241 T12307 T12279 auxpass were,recorded
R8242 T12308 T12309 punct (,listed
R8243 T12309 T12279 parataxis listed,recorded
R8244 T12310 T12311 det the,latter
R8245 T12311 T12309 nsubjpass latter,listed
R8246 T12312 T12309 auxpass are,listed
R8247 T12313 T12309 prep in,listed
R8248 T12314 T12315 compound Table,S3
R8249 T12315 T12313 pobj S3,in
R8250 T12316 T12309 punct ),listed
R8251 T12317 T12279 punct .,recorded

craft-ca-core-ex-dev

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T12718 214-217 CHEBI:37987 denotes Cy3
T12719 221-224 CHEBI:37989 denotes Cy5
T12720 722-725 CHEBI:37987 denotes Cy3
T12721 726-729 CHEBI:37989 denotes Cy5
T12722 1029-1032 _FRAGMENT denotes up-
T12723 1041-1050 GO_EXT:positive_regulation denotes regulated
T12724 1036-1050 GO_EXT:negative_regulation denotes down-regulated
T12725 1051-1056 SO_EXT:0000704 denotes genes
R8551 T12723 T12722 _lexicallyChainedTo regulated,up-

craft-ca-core-dev

Below, discontinuous spans are shown in the chain model. You can change it to the bag model.

Id Subject Object Predicate Lexical cue
T12660 214-217 CHEBI:37987 denotes Cy3
T12661 221-224 CHEBI:37989 denotes Cy5
T12662 722-725 CHEBI:37987 denotes Cy3
T12663 726-729 CHEBI:37989 denotes Cy5
T12664 1051-1056 SO:0000704 denotes genes