nature geoscience | www.nature.com/naturegeoscience. 1. Supplementary Information. External forcing as a metronome for Atlantic multidecadal variability.
used in muscle electroporation experiments and in protein degradation .... 8.0) and subsequently blocked in 5% nonfat milk (Protifar Plus, Nutricia) in TBS.
Supplementary Table 2: primers sequences for InTag adaptor generation ... BGHpA: the bovine growth hormone polyadenylation signal, CmR: chloramphenicol ...
Supplementary Figure 1 Comparison of CBM40 crystal structures indicating conservation ... These were used to create the tree in Fig 3. Sequence ... Positions of the conserved binding sites in this alignment are as follows (with corresponding .... Num
(www.imgt/cines.org) was used to analyze the IGHV sequences obtained; ... IGHV germline identity
Animals and Samples collection. Frozen postmortem brain tissue samples from rhesus macaque were provided by Kunming. Primate Research Center of the ...
the determination of antioxidase activities and F2-isoprostane levels, respectively. The tissue preparation for the determination of antioxidase activity was ...
No gross skeletal abnormalities. Misplaced chondrocytes near perichondrium in ribs. Loss of columnar organization in proliferating zone. (4). Col2-rtTA-Cre;Ext1 ...
Aug 8, 2016 - terminus of GP1 (blue) with the fusion loop (red) and T-loop (orange) of GP2. Cysteine pairs are shown as purple spheres. The role, if any, ...
NPxxY (Asn322-Tyr326 in D1r) region rmsd to frame 0 (start of the ..... bis(diphenylphosphino)ferrocene]dichloropalladium(II) (6.0 g, 8.2 mmol), ..... tricyclohexylphosphine (99%, 128 mg, 0.452 mmol) and palladium(II) acetate (101 mg, 0.450.
incubation at 4°C. Beads were washed and six rounds of depletion were performed for 20 ... Baculoviruses expressing FLAG-xlFANCJ were produced using the ...
63o scattering angle and the geometry is such that the scattering ... When fitting the Thomson scattering data, a 0.025 nm instrument function was ... an average value of ne â¼ 1020 cmâ3 and assuming Te â¼ 450 eV, we get âTe/Te ... In order to
amplification with the primers pGADT-linker-gamma-F2 and pGADT-Gpb-R2, ..... Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, ...
Supplementary Figure 1: The absolute OCR profiles for the data presented in Figure 1. The vertical dotted lines ... 350 450 550 960 980 1000. BDQ. TIME (min).
a Department of Materials Science and Engineering, College of Engineering, Seoul ... b Department of Mechanical Engineering, Stanford University, California ...
Supplementary Materials. The biochemical basis for thermoregulation in heat-producing flowers. Yui Umekawa1, Roger S. Seymour2, and Kikukatsu Ito1, 3*.
for a standard sensitizer, rose bengal (quantum yield, 75% in D2O3). The quantum yield of singlet oxygen in Q- depleted RCs from Rb. sphaeroides R-26 was ...
Dec 21, 2013 - Longb Liao, Qiuhui Zhang, Zhihua Su, Zhongzheng Zhao, Yanan Wang, Yang Li,. Xiaoxiang Lu, Dongguang Wei, Guoying Feng, Qingkai Yu, ...
The definition of Shannon's entropy S for a (discrete) random variable X reads [6, 7]:. S = â ..... is that the strategy permits to deal with an uncertain environment.
properties of snow that cause the O2/N2 fractionation may also be affected by factors other than the ..... Antro del Corchia cave (Italy) record at 129±1 kyr BPS7.
Orbital specific chirality and homochiral self-assembly of achiral molecules induced by charge transfer and spontaneous symmetry breaking. A. Mugarza. 1.
... 1 M NaTFSI in PC electrolyte at a current density of 0.1 C. ...... Effect of fluoroethylene carbonate on electrochemical performances of lithium electrodes and ...
PHP front-end to a MySQL database. Figure T1 shows an example of a more complex query. In ... Figure T1. Gene Ontology Database Advance Search Option.
Supplementary Information: Tutorial The Gene Ontology Specificity Quantifier Database allows for simple as well as more complex (compound) queries. The Gene Ontology Specificity Quantifier Database was written with a PHP front-end to a MySQL database. Figure T1 shows an example of a more complex query. In this example, the search involves membrane-related genes with a desire for more general term (information less than 4 bits). The search is narrowed to the cell component branch of the Gene Ontology.
As shown in Figure T2, information can be projected onto a scale from general terms (low bits) to high specify (large number of bits). Using this information, gene sets can be partitioned into unbiased sets- with information distributed more evenly across the set (than by using the Gene Ontology’s graphical structure as a proxy for specificity).
Figure T2. Gene Ontology Terms on an Information Theoretic Scale
The results are shown in Figure T3. From here, the user can see which partitions (ref) a particular GO term belongs to as well as various information theoretic metrics used to determine this. The user can then print or export the results to a variety of formats, including XML, Excel, CSV, and Word (see Figure T4 and Figure T5). Figure T6 shows an example of exporting to Excel.
Figure T3. Gene Ontology Database Results
Figure T4. Ontology Database Print Option
Figure T5. Gene Ontology Database Export Option
Figure T6. Gene Ontology Database Export Option to Excel
An example of how GO can be partitioned into a set of nodes with similar information (8 nodes in this case) is shown in Figure T7 (with the numbers representing GO identifiers for the unselected nodes). An example of the improvement in selecting uniform partitions is shown in Figure T8. These show histograms of GO level nodes versus GO partitions with a tighter distribution for the GO partition-based information compared to that of graphical structure-derived GO level node information.
Figure T7. An 8-node GO Partition
Figure T8. Histogram of GO Level 2 Versus GO Partitions Level 2
An example of using partitions for analysis is described next. This example uses the “HOX_LIST_JP” set from Gene Set Enrichment Analysis (GSEA) dataset. This data contains HOX proteins involved in hematopoiesis. Figure T9 shows the 6-node GO term partition applied to this set. Several findings are apparent: “regulation of metabolism” and “transcription” are highly enriched, and their p-values are confirmed to be 1.38 x 10-38 and 7.91 x 10-38 respectively. However, several smaller clusters of proteins exist within this set, which correspond to annotation with the “response to stimulus,” “organismal physiological process,” and “biopolymer metabolism” nodes. Thus, Figure T9 demonstrates what appear to be several functional subclassifications of HOX genes.
P28062 Q9UJM3
P52951
Q03014
Q92826
biopolymer metabolism
organismal physiological process
response to stimulus
Q9NYY1
O00257Q9HC52
P14652
Q15910
P35226
Q15022
transport
P35227
Q92800
O43248
P17482
P35452
P20719 P40424 P09067
P31267
P31260 P09016
O00470
Q96GD3
regulation of metabolism Q9NYD6
Q8IXJ9
P09629
Q92988
P31268
P14651
P31276 P17509
Q9UQR0
P31249
P31273 O43365
P54821
transcription
P28358
P28356
P35453
P31269
O43364
P31270
Q14774 P09017 P50458
Q9UN30
P31277
Q00056
Figure T9. Using a 6-node GO term partition, visual gene enrichment for regulation metabolism and transcription is evident in these HOX proteins involved in hematopoiesis.
