Thaps_bicluster_0141 Residual: 0.18
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_0141 0.18 Thalassiosira pseudonana
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 12 of 12
" class="views-fluidgrid-wrapper clear-block">
12971 WD40 superfamily

12971 - WD40 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

12971
22441 hypothetical protein

22441 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22441
22499 TrmA

22499 - TrmA

GO Terms:

GO:0000150, GO:0006310

CD Domains:

Go To Gene Page:

22499
23210 hypothetical protein

23210 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23210
23336 SRP40_C superfamily

23336 - SRP40_C superfamily

GO Terms:

GO:0004308

CD Domains:

Go To Gene Page:

23336
25120 U3_assoc_6 superfamily

25120 - U3_assoc_6 superfamily

GO Terms:

GO:0005622, GO:0006396

CD Domains:

Go To Gene Page:

25120
261145 Lactamase_B superfamily

261145 - Lactamase_B superfamily

GO Terms:

GO:0042781

CD Domains:

Go To Gene Page:

261145
262018 hypothetical protein

262018 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

262018
32158 NOC3

32158 - NOC3

GO Terms:

NA

CD Domains:

Go To Gene Page:

32158
34021 Methyltrn_RNA_3

34021 - Methyltrn_RNA_3

GO Terms:

NA

CD Domains:

Go To Gene Page:

34021
34176 AdoMet_MTases superfamily

34176 - AdoMet_MTases superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

34176
38662 BING4CT

38662 - BING4CT

GO Terms:

GO:0004812, GO:0005524, GO:0006418

CD Domains:

Go To Gene Page:

38662
GO ID Go Term p-value q-value Cluster
GO:0006310 DNA recombination 0.0117404 1 Thaps_bicluster_0141
GO:0006418 tRNA aminoacylation for protein translation 0.0349447 1 Thaps_bicluster_0141
GO:0006396 RNA processing 0.0355504 1 Thaps_bicluster_0141
Log in to post comments