Dataset mE2_34_mRNA_expression_clusters

General Information
Name	mE2_34_mRNA_expression_clusters	Species	D. melanogaster
Dataset type	gene expression cluster	FlyBase ID	FBlc0000358
Source & Content
Consists of	Clusters of genes with similar mRNA expression dynamics across development. (The modENCODE Consortium, 2010)
Created by
Available from
Strain
Stage & tissue

Cell Line
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
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FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Description & Members
Description	Gene expression level across development was determined from RNA-Seq coverage data. Genes were clustered into groups with similar expression dynamics. 34 distinct clusters were identified, representing a variety of developmental gene expression patterns. (The modENCODE Consortium, 2010)
Parent collections	modENCODE_mRNA-Seq_U
Component collection(s)	mE2_34_mRNA_expression_cluster_00 mE2_34_mRNA_expression_cluster_01 mE2_34_mRNA_expression_cluster_02 mE2_34_mRNA_expression_cluster_03 mE2_34_mRNA_expression_cluster_04 mE2_34_mRNA_expression_cluster_05 mE2_34_mRNA_expression_cluster_06 mE2_34_mRNA_expression_cluster_07 mE2_34_mRNA_expression_cluster_08 mE2_34_mRNA_expression_cluster_09 mE2_34_mRNA_expression_cluster_10 mE2_34_mRNA_expression_cluster_11 mE2_34_mRNA_expression_cluster_12 mE2_34_mRNA_expression_cluster_13 mE2_34_mRNA_expression_cluster_14 mE2_34_mRNA_expression_cluster_15 mE2_34_mRNA_expression_cluster_16 mE2_34_mRNA_expression_cluster_17 mE2_34_mRNA_expression_cluster_18 mE2_34_mRNA_expression_cluster_19 mE2_34_mRNA_expression_cluster_20 mE2_34_mRNA_expression_cluster_21 mE2_34_mRNA_expression_cluster_22 mE2_34_mRNA_expression_cluster_23 mE2_34_mRNA_expression_cluster_24 mE2_34_mRNA_expression_cluster_25 mE2_34_mRNA_expression_cluster_26 mE2_34_mRNA_expression_cluster_27 mE2_34_mRNA_expression_cluster_28 mE2_34_mRNA_expression_cluster_29 mE2_34_mRNA_expression_cluster_30 mE2_34_mRNA_expression_cluster_31 mE2_34_mRNA_expression_cluster_32 mE2_34_mRNA_expression_cluster_33
Number in collection
Comment on number in collection
Members
Experimental protocol
Vector
Sample preparation	See report for modENCODE_mRNA-Seq_U. (The modENCODE Consortium, 2010)
Collection preparation	See report for modENCODE_mRNA-Seq_U. (The modENCODE Consortium, 2010)
Mode of assay	See report for modENCODE_mRNA-Seq_U. (The modENCODE Consortium, 2010)
Assay platform	See report for modENCODE_mRNA-Seq_U. (The modENCODE Consortium, 2010)
Data analysis	Genes were probabilistically assigned to one of 34 expression clusters. (modENCODE Consortium et al., 2010) The developmental expression profiles of 10,733 genes, as annotated in FlyBase release 5.22 (October 2009), were clustered using a Gaussian mixture model, which assumes that genes within each cluster are distributed according to a Gaussian distribution. The parameters of each cluster, a mean and a covariance matrix were estimated based on expectation maximization. The data were pre-processed as follows: add 1 to each expression value, log transform and standardize. The number of clusters, k, to maximize the penalized log likelihood of hold out data. The result of clustering is a probability that a gene belongs to a particular cluster. A gene was assigned to the cluster with the highest probability value. (The modENCODE Consortium, 2010)
Additional data

Associated files
Additional sites
Comments
	GO term enrichment and motif enrichment of each cluster is presented in fig. S15 (FBrf0213506). (The modENCODE Consortium, 2010)
Synonyms & Secondary IDs
Reported As
Symbol Synonym	34 expression clusters (modENCODE Consortium et al., 2010) clustered expression profiles (The modENCODE Consortium, 2010) co-expression clusters (FlyBase Genome Annotators, 2011) Gene co-expression clusters (The modENCODE Consortium, 2010) mE2_34_mRNA_expression_clusters
Secondary FlyBase IDs

References ( 4 )
Research paper	modENCODE Consortium et al., 2010, Science 330(6012): 1787--1797 Identification of functional elements and regulatory circuits by Drosophila modENCODE. [FBrf0212741]
Supplementary material	The modENCODE Consortium, 2010, Science 330(6012): DataS14: Gene co-expression clusters. [FBrf0213979] The modENCODE Consortium, 2010, Science 330(6012): Supporting Online Material for Identification of Functional Elements and Regulatory Circuits by Drosophila modENCODE. [FBrf0213506]
FlyBase analysis	FlyBase Genome Annotators, 2011, Analysis and update of genes grouped into 34 co-expression clusters by the modENCODE Consortium. Analysis and update of genes grouped into 34 co-expression clusters by the modENCODE Consortium. [FBrf0214035]