JMB Proof for Manuscript #5219

Beyond Synexpression Relationships: Local 
Clustering of Time-shifted and Inverted Gene
Expression ProĈles IdentiĈes New, Biologically
Relevant Interactions

J. Qian, M. Dolled-Filhart, J. Lin
H. Yu and M. Gerstein

			Author query
			~~~~~~~~~~~~

Please complete reference 12
	please remove Qian, J. from the authors list
	the publication is in press
	the revised reference entry is as follows:
	"Jansen, R., Greenbaum, D. & Gerstein M. Relating whole-genome 
	expression data with protein-protein interactions. (in press)."

Town of Publisher for reference 27
	The town for "Plenum Press" is "New York".

6 authors then et al. - references 52
	The full author list is as follows:
	"Uetz P., Giot L., Cagney G., Mansfield T.A., Judson R.S., 
	Knight J.R., Lockshon D., Narayan V., Srinivasan M., Pochart P.,
	Qureshi-Emili A., Li Y., Godwin B., Conover D., Kalbfleisch T., 
	Vijayadamodar G., Yang M., Johnston M., Fields S., Rothberg J.M."


6 authors then et al. - references 53
	The full author list is as follows:
	"Ito T., Tashiro K., Muta S., Ozawa R., Chiba T., Nishizawa M., 
	Yamamoto K., Kuhara S., Sakaki Y."
	
	
Word missing pg. 9
	we were able to locate the error

                         Changes to the Proofs
                         ~~~~~~~~~~~~~~~~~~~~~
N.B. <1a> means correction A on page 1.


<1a> [pg 1, second to last line]
	please add "http://" to bioinfo web address
	no spaces after each "/"
	to read "http://bioinfo.mbb.yale.edu/expression/cluster"

<1b> [pg 1, last line]
	please add "http://www." to genecensus web address
	to read "http://www.genecensus.org/expression/cluster"

<2>  [pg 2, right column, last line] 
	please hyphenate "time-shifted"

<3a> [pg 3, figure caption of Figure 1, line 1]
	please replace "Two" with "Three"
	to read "Fig 1. Three examples showing"

<3b> [pg 3, figure caption of Figure 1, lines 2-3]
	please place subfigure label before word
	to read "(a) simultaneous, (b) time-delayed, and (c) inverted relationships"

<3c> [pg 3, left column, last line]
	please remove period before footnote 31
	to read "dataset 31 and a less extensive..."

<4a> [pg 4, right column, second paragraph, last line]
	please replace "are" with "were"
	to read "5991 genes were included..."

<4b> [pg 4, right column, fourth paragrph, 5th to last line]
	please add comma after "Then"
	to read "data). Then, for further..."

<5a> [pg 5, right column, second paragraph, last two lines]
	please remove all spaces after "/"
	to read "http://bioinfo.mbb.yale.edu/expression/cluster or
	http://www.genecensus.org/expression/cluster"

<5b> [pg 5, right column, third paragraph, 10th to last line]
	remove "m" from after "YMR320"
	to read "YMR320 and YKL177W are joined..."

<5b> [pg 5, right column, third paragraph, 5th to last line]
	please lowercase word "Figure"
	to read "the figure, which are very small"

<5c> [pg 5, right column, last paragraph, 4th line]
	please replace word "quantities" with "global statistics"
	to read "global statistics. We calculate..."

<6a> [pg 6, figure caption for Figure 3, line 1]
	please lowercase "Figure"
	to read "algorithm. This figure was prepared..." 

<6a> [pg 6, figure caption for Figure 3, line 2]
	please remove all spaces following "/" in web address
	to read "http://www.mpi-sb.mpg.de/AGD"

<7a> [pg 7, figure 4]
	please make sure the figure is in color
	so that red will be distinguished from black

<7b> [pg 7, left column]
	please decrease large spacing before heading "Examples of Relationships..."

<9>  [pg 9, figure caption of Figure 6, left column, 7th last line]
	please replace "15" with "16" and "16" with "10"
	to read "with match score 16 is 10/1000 =0.01,..."

<10> [pg 10, right column, 5th to last line]
	please replace "proportionately" with "proportionally"
	to read "it seems we found proportionally..."

<11> [pg 11, Table 1, line 1]
	please lower case "Table"
	to read "The table also gives..."

<12> [pg 12, right column, 4th paragraph]
	please move "most usefully" to after "applied"
	to read "Local clustering can be applied most usefully to..."