This was evident in our study as well where we showed that in general the variance in technical replicates was low, with an overall narrow distribution across the peptides quantified. Red points are those correlations which were significant for transcripts only, green points are those correlations which were significant for protein data only and black points are those which were not significant in either of the two datasets.
A similar comparative analysis of molecular phenotype mapping in Arabidopsis  was reported subsequently. Herein, we used transcriptomic, proteomic, and hormone analyses to investigate the key candidate genes/proteins in loquat (Eriobotrya japonica) at the stages of flower bud differentiation (FBD), floral bud elongation (FBE), and floral anthesis (FA). 2002. https://doi.org/10.1371/journal.pgen.1001393.g006, https://doi.org/10.1371/journal.pgen.1001393.t002. A de novo tentacle transcriptome, containing more than 23,000 contigs, was constructed and used in proteomic analysis of C. fuscescens venom to identify potential toxins. The genomic exon coordinates for each peptide was then used to query the Ensembl database to acquire the Ensembl Gene IDs. We complemented the LC/MS studies for a small set of proteins (11) by performing immunoblot quantitation in 9 of the HMDP strains. The significance of the observed average p-values for each GO term is reported as the two-tailed test against the empirical distribution created by the corresponding 100,000 permutation set. Combined proteome and transcriptome analyses for the discovery of urinary biomarkers for urothelial carcinoma. Prior to the LC-MS analysis 3.75 ug aliquots from each individual sample were mixed with the same amount of 18O-labeled reference sample. We discuss these points in turn below. In the protein data, mitochondrial genes were overwhelmingly the largest set and in the transcript data the nuclear compartment was at the top of the list for enriched CC GO terms. Since the transcript and protein data have different variance properties, which may subsequently affect our statistical power to detect associations in the two different datasets, we avoided the use of the same statistical cutoff for each dataset. The ligated products were then separated on 2% agarose gel, 200 bp fragments were selected and PCR amplified using PE 1.0 and PE 2.0, and purified using QIAquick PCR Purification Kit (QIAGEN, part # 28104). Upon the success of this, scientists moved on to characterizing the total protein contents in animals such as guinea pigs and mice. In the transcript data, the median eQTL number/window was 8 and the highest number of associations was found for bins on Chr 4 (from 98.7 Mb to 100.8 Mb) with 71 eQTLs, Chr 5 (from 80 Mb to 83.1 Mb, from 112.4 Mb to 114.4 Mb) with 79 and 75 eQTLs in each respectively, Chr 7 (from 143.2 Mb to 146.2 Mb) with 78 eQTLs, Chr 8 (from 93.0 Mb to 95.1 Mb) with 71 eQTLs, Chr 17 (from 43.8 Mb to 46.4 Mb) with 80 eQTLs, and Chr 18 (from 55.0 Mb to 57.5 Mb) with 76 eQTLs. 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