Id |
Subject |
Object |
Predicate |
Lexical cue |
T5606 |
0-13 |
NN |
denotes |
Normalisation |
T5607 |
42-46 |
VBN |
denotes |
done |
T5608 |
14-16 |
IN |
denotes |
of |
T5609 |
17-20 |
DT |
denotes |
the |
T5610 |
32-37 |
NN |
denotes |
level |
T5611 |
21-31 |
NN |
denotes |
expression |
T5612 |
38-41 |
VBD |
denotes |
was |
T5613 |
47-52 |
VBG |
denotes |
using |
T5614 |
53-63 |
NNP |
denotes |
Affymetrix |
T5615 |
73-76 |
NN |
denotes |
MAS |
T5616 |
64-72 |
NN |
denotes |
software |
T5617 |
77-78 |
CD |
denotes |
5 |
T5618 |
78-80 |
, |
denotes |
, |
T5619 |
80-85 |
WDT |
denotes |
which |
T5620 |
89-94 |
VBN |
denotes |
based |
T5621 |
86-88 |
VBZ |
denotes |
is |
T5622 |
95-97 |
IN |
denotes |
on |
T5623 |
98-104 |
JJ |
denotes |
global |
T5624 |
105-112 |
NN |
denotes |
scaling |
T5625 |
113-115 |
IN |
denotes |
of |
T5626 |
116-121 |
JJ |
denotes |
total |
T5627 |
138-143 |
NN |
denotes |
level |
T5628 |
122-126 |
NN |
denotes |
gene |
T5629 |
127-137 |
NN |
denotes |
expression |
T5630 |
144-147 |
IN |
denotes |
per |
T5631 |
148-158 |
NN |
denotes |
microarray |
T5632 |
158-159 |
. |
denotes |
. |
T5633 |
159-237 |
sentence |
denotes |
The normalised expression values were imported to and analysed by dCHIP [24]. |
T5634 |
160-163 |
DT |
denotes |
The |
T5635 |
186-192 |
NNS |
denotes |
values |
T5636 |
164-174 |
JJ |
denotes |
normalised |
T5637 |
175-185 |
NN |
denotes |
expression |
T5638 |
198-206 |
VBN |
denotes |
imported |
T5639 |
193-197 |
VBD |
denotes |
were |
T5640 |
207-209 |
IN |
denotes |
to |
T5641 |
210-213 |
CC |
denotes |
and |
T5642 |
214-222 |
VBN |
denotes |
analysed |
T5643 |
223-225 |
IN |
denotes |
by |
T5644 |
226-231 |
NN |
denotes |
dCHIP |
T5645 |
232-233 |
-LRB- |
denotes |
[ |
T5646 |
233-235 |
CD |
denotes |
24 |
T5647 |
235-236 |
-RRB- |
denotes |
] |
T5648 |
236-237 |
. |
denotes |
. |
T5649 |
237-560 |
sentence |
denotes |
Differentially expressed genes were identified by defining the appropriate filtering criteria in the dCHIP software as: lower 90% confidence boundary of fold change between the group means exceeded twofold; the absolute difference between the two groups exceeded 100; the P value threshold of the unpaired t-test was 0.05. |
T5650 |
238-252 |
RB |
denotes |
Differentially |
T5651 |
253-262 |
VBN |
denotes |
expressed |
T5652 |
263-268 |
NNS |
denotes |
genes |
T5653 |
274-284 |
VBN |
denotes |
identified |
T5654 |
269-273 |
VBD |
denotes |
were |
T5655 |
285-287 |
IN |
denotes |
by |
T5656 |
288-296 |
VBG |
denotes |
defining |
T5657 |
297-300 |
DT |
denotes |
the |
T5658 |
323-331 |
NNS |
denotes |
criteria |
T5659 |
301-312 |
JJ |
denotes |
appropriate |
T5660 |
313-322 |
NN |
denotes |
filtering |
T5661 |
332-334 |
IN |
denotes |
in |
T5662 |
335-338 |
DT |
denotes |
the |
T5663 |
345-353 |
NN |
denotes |
software |
T5664 |
339-344 |
NN |
denotes |
dCHIP |
T5665 |
354-356 |
IN |
denotes |
as |
T5666 |
356-358 |
: |
denotes |
: |
T5667 |
358-363 |
JJ |
denotes |
lower |
T5668 |
366-367 |
NN |
denotes |
% |
T5669 |
364-366 |
CD |
denotes |
90 |
T5670 |
379-387 |
NN |
denotes |
boundary |
T5671 |
368-378 |
NN |
denotes |
confidence |
T5672 |
427-435 |
VBN |
denotes |
exceeded |
T5673 |
388-390 |
IN |
denotes |
of |
T5674 |
391-395 |
NN |
denotes |
fold |
T5675 |
396-402 |
NN |
denotes |
change |
T5676 |
403-410 |
IN |
denotes |
between |
T5677 |
411-414 |
DT |
denotes |
the |
T5678 |
421-426 |
NNS |
denotes |
means |
T5679 |
415-420 |
NN |
denotes |
group |
T5680 |
551-554 |
VBD |
denotes |
was |
T5681 |
436-443 |
RB |
denotes |
twofold |
T5682 |
443-444 |
: |
denotes |
; |
T5683 |
445-448 |
DT |
denotes |
the |
T5684 |
458-468 |
NN |
denotes |
difference |
T5685 |
449-457 |
JJ |
denotes |
absolute |
T5686 |
492-500 |
VBD |
denotes |
exceeded |
T5687 |
469-476 |
IN |
denotes |
between |
T5688 |
477-480 |
DT |
denotes |
the |
T5689 |
485-491 |
NNS |
denotes |
groups |
T5690 |
481-484 |
CD |
denotes |
two |
T5691 |
501-504 |
CD |
denotes |
100 |
T5692 |
504-505 |
: |
denotes |
; |
T5693 |
506-509 |
DT |
denotes |
the |
T5694 |
518-527 |
NN |
denotes |
threshold |
T5695 |
510-511 |
NN |
denotes |
P |
T5696 |
512-517 |
NN |
denotes |
value |
T5697 |
528-530 |
IN |
denotes |
of |
T5698 |
531-534 |
DT |
denotes |
the |
T5699 |
546-550 |
NN |
denotes |
test |
T5700 |
535-543 |
JJ |
denotes |
unpaired |
T5701 |
544-545 |
NN |
denotes |
t |
T5702 |
545-546 |
HYPH |
denotes |
- |
T5703 |
555-559 |
CD |
denotes |
0.05 |
T5704 |
559-560 |
. |
denotes |
. |
T5705 |
560-706 |
sentence |
denotes |
The false discovery rate was established with a permutation test for each pairwise comparison to estimate the proportion of false-positive genes. |
T5706 |
561-564 |
DT |
denotes |
The |
T5707 |
581-585 |
NN |
denotes |
rate |
T5708 |
565-570 |
JJ |
denotes |
false |
T5709 |
571-580 |
NN |
denotes |
discovery |
T5710 |
590-601 |
VBN |
denotes |
established |
T5711 |
586-589 |
VBD |
denotes |
was |
T5712 |
602-606 |
IN |
denotes |
with |
T5713 |
607-608 |
DT |
denotes |
a |
T5714 |
621-625 |
NN |
denotes |
test |
T5715 |
609-620 |
NN |
denotes |
permutation |
T5716 |
626-629 |
IN |
denotes |
for |
T5717 |
630-634 |
DT |
denotes |
each |
T5718 |
644-654 |
NN |
denotes |
comparison |
T5719 |
635-643 |
JJ |
denotes |
pairwise |
T5720 |
655-657 |
TO |
denotes |
to |
T5721 |
658-666 |
VB |
denotes |
estimate |
T5722 |
667-670 |
DT |
denotes |
the |
T5723 |
671-681 |
NN |
denotes |
proportion |
T5724 |
682-684 |
IN |
denotes |
of |
T5725 |
685-690 |
JJ |
denotes |
false |
T5726 |
691-699 |
JJ |
denotes |
positive |
T5727 |
690-691 |
HYPH |
denotes |
- |
T5728 |
700-705 |
NNS |
denotes |
genes |
T5729 |
705-706 |
. |
denotes |
. |
R1597 |
T5606 |
T5607 |
nsubjpass |
Normalisation,done |
R1598 |
T5608 |
T5606 |
prep |
of,Normalisation |
R1599 |
T5609 |
T5610 |
det |
the,level |
R1600 |
T5610 |
T5608 |
pobj |
level,of |
R1601 |
T5611 |
T5610 |
compound |
expression,level |
R1602 |
T5612 |
T5607 |
auxpass |
was,done |
R1603 |
T5613 |
T5607 |
advcl |
using,done |
R1604 |
T5614 |
T5615 |
compound |
Affymetrix,MAS |
R1605 |
T5615 |
T5613 |
dobj |
MAS,using |
R1606 |
T5616 |
T5615 |
compound |
software,MAS |
R1607 |
T5617 |
T5615 |
nummod |
5,MAS |
R1608 |
T5618 |
T5615 |
punct |
", ",MAS |
R1609 |
T5619 |
T5620 |
dep |
which,based |
R1610 |
T5620 |
T5615 |
relcl |
based,MAS |
R1611 |
T5621 |
T5620 |
auxpass |
is,based |
R1612 |
T5622 |
T5620 |
prep |
on,based |
R1613 |
T5623 |
T5624 |
amod |
global,scaling |
R1614 |
T5624 |
T5622 |
pobj |
scaling,on |
R1615 |
T5625 |
T5624 |
prep |
of,scaling |
R1616 |
T5626 |
T5627 |
amod |
total,level |
R1617 |
T5627 |
T5625 |
pobj |
level,of |
R1618 |
T5628 |
T5629 |
compound |
gene,expression |
R1619 |
T5629 |
T5627 |
compound |
expression,level |
R1620 |
T5630 |
T5627 |
prep |
per,level |
R1621 |
T5631 |
T5630 |
pobj |
microarray,per |
R1622 |
T5632 |
T5607 |
punct |
.,done |
R1623 |
T5634 |
T5635 |
det |
The,values |
R1624 |
T5635 |
T5638 |
nsubjpass |
values,imported |
R1625 |
T5636 |
T5635 |
amod |
normalised,values |
R1626 |
T5637 |
T5635 |
compound |
expression,values |
R1627 |
T5639 |
T5638 |
auxpass |
were,imported |
R1628 |
T5640 |
T5638 |
prep |
to,imported |
R1629 |
T5641 |
T5638 |
cc |
and,imported |
R1630 |
T5642 |
T5638 |
conj |
analysed,imported |
R1631 |
T5643 |
T5642 |
prep |
by,analysed |
R1632 |
T5644 |
T5642 |
dobj |
dCHIP,analysed |
R1633 |
T5645 |
T5646 |
punct |
[,24 |
R1634 |
T5646 |
T5642 |
parataxis |
24,analysed |
R1635 |
T5647 |
T5646 |
punct |
],24 |
R1636 |
T5648 |
T5638 |
punct |
.,imported |
R1637 |
T5650 |
T5651 |
advmod |
Differentially,expressed |
R1638 |
T5651 |
T5652 |
amod |
expressed,genes |
R1639 |
T5652 |
T5653 |
nsubjpass |
genes,identified |
R1640 |
T5654 |
T5653 |
auxpass |
were,identified |
R1641 |
T5655 |
T5653 |
prep |
by,identified |
R1642 |
T5656 |
T5655 |
pcomp |
defining,by |
R1643 |
T5657 |
T5658 |
det |
the,criteria |
R1644 |
T5658 |
T5656 |
dobj |
criteria,defining |
R1645 |
T5659 |
T5658 |
amod |
appropriate,criteria |
R1646 |
T5660 |
T5658 |
compound |
filtering,criteria |
R1647 |
T5661 |
T5656 |
prep |
in,defining |
R1648 |
T5662 |
T5663 |
det |
the,software |
R1649 |
T5663 |
T5661 |
pobj |
software,in |
R1650 |
T5664 |
T5663 |
compound |
dCHIP,software |
R1651 |
T5665 |
T5656 |
prep |
as,defining |
R1652 |
T5666 |
T5665 |
punct |
: ,as |
R1653 |
T5667 |
T5668 |
amod |
lower,% |
R1654 |
T5668 |
T5670 |
compound |
%,boundary |
R1655 |
T5669 |
T5668 |
nummod |
90,% |
R1656 |
T5670 |
T5672 |
nsubj |
boundary,exceeded |
R1657 |
T5671 |
T5670 |
compound |
confidence,boundary |
R1658 |
T5672 |
T5680 |
ccomp |
exceeded,was |
R1659 |
T5673 |
T5670 |
prep |
of,boundary |
R1660 |
T5674 |
T5675 |
compound |
fold,change |
R1661 |
T5675 |
T5673 |
pobj |
change,of |
R1662 |
T5676 |
T5670 |
prep |
between,boundary |
R1663 |
T5677 |
T5678 |
det |
the,means |
R1664 |
T5678 |
T5676 |
pobj |
means,between |
R1666 |
T5680 |
T5665 |
pcomp |
was,as |
R1667 |
T5681 |
T5672 |
advmod |
twofold,exceeded |
R1668 |
T5682 |
T5680 |
punct |
;,was |
R1669 |
T5683 |
T5684 |
det |
the,difference |
R1670 |
T5684 |
T5686 |
nsubj |
difference,exceeded |
R1672 |
T5686 |
T5680 |
ccomp |
exceeded,was |
R1675 |
T5689 |
T5687 |
pobj |
groups,between |
R1676 |
T5690 |
T5689 |
nummod |
two,groups |
R1677 |
T5691 |
T5686 |
dobj |
100,exceeded |
R1678 |
T5692 |
T5680 |
punct |
;,was |
R1679 |
T5693 |
T5694 |
det |
the,threshold |
R1680 |
T5694 |
T5680 |
nsubj |
threshold,was |
R1683 |
T5697 |
T5694 |
prep |
of,threshold |
R1684 |
T5698 |
T5699 |
det |
the,test |
R1685 |
T5699 |
T5697 |
pobj |
test,of |
R1689 |
T5703 |
T5680 |
attr |
0.05,was |
R1690 |
T5704 |
T5653 |
punct |
.,identified |
R1691 |
T5706 |
T5707 |
det |
The,rate |
R1692 |
T5707 |
T5710 |
nsubjpass |
rate,established |
R1693 |
T5708 |
T5709 |
amod |
false,discovery |
R1694 |
T5709 |
T5707 |
compound |
discovery,rate |
R1695 |
T5711 |
T5710 |
auxpass |
was,established |
R1696 |
T5712 |
T5710 |
prep |
with,established |
R1697 |
T5713 |
T5714 |
det |
a,test |
R1698 |
T5714 |
T5712 |
pobj |
test,with |
R1699 |
T5715 |
T5714 |
compound |
permutation,test |
R1700 |
T5716 |
T5714 |
prep |
for,test |
R1701 |
T5717 |
T5718 |
det |
each,comparison |
R1702 |
T5718 |
T5716 |
pobj |
comparison,for |
R1703 |
T5719 |
T5718 |
amod |
pairwise,comparison |
R1704 |
T5720 |
T5721 |
aux |
to,estimate |
R1705 |
T5721 |
T5710 |
advcl |
estimate,established |
R1706 |
T5722 |
T5723 |
det |
the,proportion |
R1707 |
T5723 |
T5721 |
dobj |
proportion,estimate |
R1708 |
T5724 |
T5723 |
prep |
of,proportion |
R1709 |
T5725 |
T5726 |
amod |
false,positive |
R1710 |
T5726 |
T5728 |
amod |
positive,genes |
R1711 |
T5727 |
T5726 |
punct |
-,positive |
R1712 |
T5728 |
T5724 |
pobj |
genes,of |
R1713 |
T5729 |
T5710 |
punct |
.,established |
R1665 |
T5679 |
T5678 |
compound |
group,means |
R1671 |
T5685 |
T5684 |
amod |
absolute,difference |
R1673 |
T5687 |
T5684 |
prep |
between,difference |
R1674 |
T5688 |
T5689 |
det |
the,groups |
R1681 |
T5695 |
T5696 |
compound |
P,value |
R1682 |
T5696 |
T5694 |
compound |
value,threshold |
R1686 |
T5700 |
T5699 |
amod |
unpaired,test |
R1687 |
T5701 |
T5699 |
compound |
t,test |
R1688 |
T5702 |
T5699 |
punct |
-,test |