Category Archives: Allergy

Allergy

Genome plots with Sigmaplot

Here are some instructions how to create genome coordinate plots with Sigmaplot. The Systat Sigmaplot FAQ recommends for this kind of figures “floating bars” that

can be created using two different mechanisms. If you just need a simple floating bar chart, you can use a box plot of two values per column. Enter the top and bottom ranges for your bars in each column, and then create a box plot…
If you need to create grouped, floating bar charts, you will need … a masking plot. Create a grouped bar chart, using the upper values of the bars. Create a second bar chart for the same graph (click the graph, then click the grouped bar chart icon from the Graph toolbar), this time, using the lower values of the bars.

None of these methods works with fill patterns. Also repeated segments (at the same level) are not possible.

So I have worked out therefore another method using a stacked bar plot:
(1) put in the first column an increasing value 1 … 10 (->gets Y axis)
(2) put into the second column zeros (->gets start set 1)
(3) third colum: first feature start (->gets end set 1)
(4) fourth column: zeros (->gets start set 2)
(5) fifth column: first feature end (->gets end set 2)
(6) and so on
(7) assign colors: white for start set 1, blue for start set 2, white for start set 3 and so on

You should then end up with a plot like this

Related posts: What’s in your genome?| How we are reshuffling our genome| First individual human genome| Human genome variation| View plink GWA results as genome browser track|

Allergy

“Science advances in stages and no story is complete”

Sometimes we think we are alone with our difficulty of getting a good paper published. In lucid moments, however, we find others making the same experience- see a commentary in Science

The stress associated with publishing experimental results–a process that can take as long as obtaining the results in the first place–can drain much of the joy from practicing science Continue reading “Science advances in stages and no story is complete” →

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Allergy, Genetics

Probability that a genetic association is false positive

An (anonymous) reviewer of our forthcoming EJHG paper on IgE and STAT3 pointed me towards a JNCI paper that has a nice supplement – an excel sheet to calculate the probability that a positive report is false. It basically relies on (i) the magnitude of the p-value (ii) statistical power and (iii) fraction of tested hypothesis. While we certainly know (i) and (ii), (iii) is always hard to know with many datasets including hundreds of traits that allow indefinite numbers of subgroups. Are you really interested in a new paper about “An African-specific functional polymorphism in KCNMB1 shows sex-specific association with asthma severity” that encompasses 1 of virtually 100 ethnic groups; 1 or virtually 25000 genes; 1 of 2 sexes; 1 or virtually 50 asthma related traits, yea, yea.

Related posts: Is there any sense of genetic association studies?| About replication validity of genetic association studies and illogical journal policies| Anonymizing genetic data| Once again genetic testing| Who is who in German genetic research?|

Allergy

View plink GWA results as genome browser track

This R script will parse plink‘s GC adjusted output to a GFF file that can be uploaded as genome browser track file. Just adjust the pathname at the beginning…

script

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19:		trait <- c("e:/QT_10s.qassoc.adjusted")
gff <- c("browser position chr5:1-1000000\n")
gff <- paste(gff,'browser hide all\n',sep="")
gff <- paste(gff,'browser pack refGene encodeRegions\n',sep="")
gff <- paste(gff,'browser full altGraph\n',sep="")
gff <- paste(gff,'track type=wiggle_0 name="',trait,'" description="26/6/08" visibility=full maxHeightPixels=30 autoScale=off viewLimits=0:8 color=0,100,200 yLineMark=7 yLineOnOff=off',sep="")
write.table(gff,file=paste(d1,trait,".gff",sep=""),row.names=FALSE,col.names=FALSE,dec=".",quote=FALSE,append=FALSE)
restab <- read.fwf(file=trait,widths=c(4,12,rep(11,8)),skip=1)
restab <- restab[,1:4]
names(restab) <- c("CHR","SNP","UNADJ","GC") 
restab[,"SNP"]<-gsub(" ","",as.character(restab[,"SNP"]))
restab[,1] <- paste("chr",restab[,1],sep="")
restab <- merge(restab,SNP, by.x="SNP", by.y="Name", all.x = FALSE, all.y = FALSE)
restab[,"Position2"] <- restab[,"Position"]+1
restab[,"GC"] <- format.pval(-log10(restab[,"GC"]),digits=1)
restab$Chromosome <- as.numeric(as.character(restab$Chromosome))
restab<-restab[order(restab$Chromosome,restab$Position),]
write.table(restab[,c("CHR","Position","Position2","GC")],file=paste(trait,".gff",sep=""),sep="\t",row.names=FALSE,col.names=FALSE,dec=".",quote=FALSE,,append=TRUE)

Related posts: New genome browser version| Genome Browser now with GADview track| A catholic view of science| A protestantic view of science| What’s in your genome?|

Allergy, Genetics, Philosophy

Will the Data Deluge Make the Scientific Method Obsolete?

A new Edge article answers this question. According to Chris Anderson, we are at “the end of science”, that is, science as we know it.

The quest for knowledge used to begin with grand theories. Now it begins with massive amounts of data. Welcome to the Petabyte Age.

Yesterday I reviewed a paper that crunches massive amount of data (and even found a new pathway for asthma). Nevertheless I was asking the question if this wishful thinking? Just take the next gene in one region and the overnext in another one and I would come up with a completely different pathway. This is all about association and not by the traditional “theorize, model, test it” way of science we have been brought along, yea, yea.

Related posts: Don’t make a move| A new analysis method for blood doping| Delusion or poor scientific hypothesis| Castrated data| U-P-S-I-D-E – data sharing policy|

Allergy

Asthma and allergy trend

Besides traditional and expensive epidemiological studies to compare disease prevalence over time, the net offers also some nice research tools – click on the thumbnail to see Google asthma trend results by today. The query counts are largely consistent with most recent scientific papers seeing the asthma epidemic now at a (high) plateau. Did the environmental risk now saturate all individuals at risk?

Related posts: Notes on asthma in Africa| Where is the asthma gene?| Vitamin D and asthma| Not all that wheezes is asthma| On mice and men with asthma|

Allergy, Genetics

The many problems of GWAs

1 Comment

genetic-future has an excellent article why the recent genome scans failed (i) alleles with small effects? (ii) population differences? (iii) epistatic interactions? (iv) cnvs more relevant than snps? (v) epigenetic inheritance? (vi) disease heterogeneity? It is a thorough review better than everything Continue reading The many problems of GWAs →

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Allergy, Vitamins

Vitamin D: A 18%! reduction in early infant mortality

A study published earlier this year in the Lancet found a 18% reduction in mortality when women obtained supplements during pregnancy until 90 days post partum including additional 800 ug retinol, 200 IU vitamin D, 10 mg vitamin E, 70 mg ascorbic acid, 1.4 mg vitamin B1, 18 mg niacin, 1.9 mg vitamin B6, 2.6 ug vitamin B12, 15 mg zinc, 2 mg copper, 65 ug selenium and 150 ug iodine. Much of the effect will be due to the vitamin D supplementation Continue reading Vitamin D: A 18%! reduction in early infant mortality →

Related posts: Dual vitamin D effects on type 1 diabetes and allergy| The history of vitamin D discovery, industrial production and marketing| Is “vitamin” D a biological hub?| Let vitamin D shine in| CD 14 now also on the vitamin+allergy list|

Allergy, Vitamins

Not all that wheezes is asthma

A new abstract at the recent ATS congress now clears the 2007 controversy between the Camargo and Gale studies on the effect of vitamin D: Wheezing is not asthma (as the atopy component is missing?). Continue reading Not all that wheezes is asthma →

Related posts: Where is the asthma gene?| Notes on asthma in Africa| Why we didn´t find the asthma gene| On mice and men with asthma| Vitamin D and asthma|

Allergy

CF and PHP at the same time

For a clinical research project I need a fast webserver that understands both COLD FUSION (for the existing database stuff) and PHP (for dokuwiki). As this is a non-commercial project, I decided for the RAILO 2.0 community version that works right out of the box as it includes the Resin webserver and the H2 database as well. Following some recommendations found on the net, php is running now with with the fastcgi option showing good acceptable performance with eAccelerator.

php.cmd

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23:		@echo off

rem install php with this option
rem msiexec /i php-5.2.6-win32-installer.msi /q ADDLOCAL=cgi,ext_php_mysqli

rem check for right version
rem php-cgi -v

rem now run php on dedicated port
php-cgi -b 8002

rem let railo know in x:\railo\conf\app-default.xml
rem  <servlet servlet-name="php"
rem           servlet-class="com.caucho.servlets.FastCGIServlet">
rem    <init>
rem      <server-address>localhost:8002</server-address>
rem    </init>
rem  </servlet>
rem  <servlet-mapping url-pattern="*.php" servlet-name="php"/>

pause
exit

Related posts: < I often only have time to read abstracts >| Living on borrowed time| Increased stand by time| You may fool all the people some of the time| For the first time two human genomes compared|

Allergy, Genetics, Vitamins

CD 14 now also on the vitamin+allergy list

Just for curiosity I am collecting a list of allergy genes that are vitamin D dependent. The list is already rather long but now there is a prominent addition: CD14. Known as asthma gene for many years the vitamin D dependency isn’t such clear. A clever analysis, however, now shows that there is an intermediate step involved Continue reading CD 14 now also on the vitamin+allergy list →

Related posts: Dual vitamin D effects on type 1 diabetes and allergy| Another path from vitamin D to allergy| Hans Selye: Ancestor of the allergy vitamin hypothesis| Is “vitamin” D a biological hub?| Link list essential photo & video & audio|

Allergy, Vitamins

Vitamin D as an adjuvans to specific immunotherapy

Despite the known allergy promoting effect of vitamin D in early childhood, there is mounting evidence that it may have beneficial effects during specific immunotherapy. A paper on “IL-10-inducing adjuvants enhance sublingual immunotherapy efficacy in a murine asthma model” by researchers from a French allergen company Continue reading Vitamin D as an adjuvans to specific immunotherapy →

Related posts: Innate immunity is species-, individual, organ-specific| Allelic specific expression| Dual vitamin D effects on type 1 diabetes and allergy| More retro vitamin D| Calcium gradient in skin, vitamin D and filaggrin|