Thaps_bicluster_0199 Residual: 0.24
Thalassiosira pseudonana

Module Page Help

What is a module?

Regulatory units (modules) in the Network Portal are based on the network inference algorithm used. For the current version, modules are based on cMonkey modules and Inferelator regulatory influences on these modules. More specifically, module refers to set of genes that are conditionally co-regulated under subset of the conditions. Identification of modules integrates co-expression, de-novo motif identification, and other functional associations such as operon information and protein-protein interactions.

Expression Profiles

Expression profiles is a plot of the expression ratios (log10) of the module's genes, over all subset of the conditions included in the module. The X-axis represent conditions and the Y-axis represents log10 expression ratios. Each gene is plotted as line plot with different colors. Colored legend for the lines are presented under the plot. This plot is dynamic. Clicking on the gene names in the legend will show/hide the plot for that particular gene. A tooltip will show expression ratio information if you mouseover the lines in the plot.

Motif Locations

Location of the Identified motifs for the module in the upstream regions of the member genes are shown under the expression profiles plot. This plot shows the diagram of the upstream positions of the motifs, colored red and green for motifs #1, and 2, respectively. Intensity of the color is proportional to the significance of the occurence of that motif at a given location. Motifs on the forward and reverse strand are represented over and under the line respectively.

Regulators

For each module, single or AND logic connected regulatory influences are listed under the regulators tab. These regulatory influences are identified by Inferelator. Table shows name of the regulator and its type. tf: Transcription factor, ef: Environmental factor and combiner:Combinatorial influence of a tf or an ef through logic gate. Tabel is sortable by clicking on the arrows next to column headers.

Motifs

Transcription factor binding motifs help to elucidate regulatory mechanism. cMonkey integrates powerful de novo motif detection to identify conditionally co-regulated sets of genes. De novo predicted motifs for each module are listed in the module page as motif logo images along with associated prediction statistics (e-values). The main module page also shows the location of these motifs within the upstream sequences of the module member genes.
Title Residual Model version Organism
Thaps_bicluster_0199 0.24 Thalassiosira pseudonana
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Displaying 1 - 18 of 18
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20658 Nop53

20658 - Nop53

GO Terms:

NA

CD Domains:

Go To Gene Page:

20658
22212 COG5638

22212 - COG5638

GO Terms:

GO:0004308

CD Domains:

Go To Gene Page:

22212
22985 WD40 superfamily

22985 - WD40 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

22985
23187 SDA1

23187 - SDA1

GO Terms:

NA

CD Domains:

Go To Gene Page:

23187
23354 RNA-binding protein of the pumilio family

23354 - RNA-binding protein of the pumilio family

GO Terms:

GO:0003723, GO:0016071

CD Domains:

Go To Gene Page:

23354
24793 DUF501 superfamily

24793 - DUF501 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

24793
24849 (Tp_CCCH8) DnaQ_like_exo superfamily

24849 - (Tp_CCCH8) DnaQ_like_exo superfamily

GO Terms:

GO:0003676, GO:0004527, GO:0005622, GO:0004518, GO:0016788, GO:0042578

CD Domains:

Go To Gene Page:

24849
25663 hypothetical protein

25663 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25663
268598 COG1094

268598 - COG1094

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

268598
268689 RRM6_RBM19_RRM5_MRD1

268689 - RRM6_RBM19_RRM5_MRD1

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

268689
268766 MdlB

268766 - MdlB

GO Terms:

GO:0005524, GO:0006810, GO:0016021, GO:0042626, GO:0016887, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

268766
269352 WD40 superfamily

269352 - WD40 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

269352
34006 Sun

34006 - Sun

GO Terms:

NA

CD Domains:

Go To Gene Page:

34006
36986 EMG1

36986 - EMG1

GO Terms:

GO:0005634, GO:0007046

CD Domains:

Go To Gene Page:

36986
37083 PTZ00037

37083 - PTZ00037

GO Terms:

GO:0006457, GO:0031072, GO:0051082

CD Domains:

Go To Gene Page:

37083
38006 FKBP_C

38006 - FKBP_C

GO Terms:

GO:0006457, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

38006
GO ID Go Term p-value q-value Cluster
GO:0007046 ribosome biogenesis 0.00412967 1 Thaps_bicluster_0199
GO:0006457 protein folding 0.00679704 1 Thaps_bicluster_0199
GO:0016071 mRNA metabolism 0.00927255 1 Thaps_bicluster_0199
GO:0006810 transport 0.176337 1 Thaps_bicluster_0199
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