Thaps_bicluster_0257 Residual: 0.20
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_0257 0.20 Thalassiosira pseudonana
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Displaying 1 - 17 of 17
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17657 HSR1_MMR1

17657 - HSR1_MMR1

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

17657
21082 Cupin_8 superfamily

21082 - Cupin_8 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21082
22404 DEXDc superfamily

22404 - DEXDc superfamily

GO Terms:

GO:0003676, GO:0005524, GO:0008026, GO:0004386, GO:0000810, GO:0004787, GO:0008722, GO:0008758, GO:0008796, GO:0008828, GO:0016462, GO:0016818, GO:0019176, GO:0019177

CD Domains:

Go To Gene Page:

22404
24016 Ebp2 superfamily

24016 - Ebp2 superfamily

GO Terms:

GO:0007046, GO:0004003, GO:0004004, GO:0008026, GO:0008094, GO:0008186, GO:0015462, GO:0015616, GO:0016887, GO:0017116, GO:0042623, GO:0042624, GO:0042625, GO:0042626

CD Domains:

Go To Gene Page:

24016
25484 hypothetical protein

25484 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25484
262275 hypothetical protein

262275 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

262275
268331 WD40

268331 - WD40

GO Terms:

GO:0004197, GO:0006508

CD Domains:

Go To Gene Page:

268331
268559 COG1084

268559 - COG1084

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

268559
27873 PLN02274

27873 - PLN02274

GO Terms:

GO:0003824, GO:0003938, GO:0006177

CD Domains:

Go To Gene Page:

27873
31710 RIO1_euk

31710 - RIO1_euk

GO Terms:

GO:0005554, GO:0004672, GO:0005524, GO:0006468

CD Domains:

Go To Gene Page:

31710
32374 TPR

32374 - TPR

GO Terms:

NA

CD Domains:

Go To Gene Page:

32374
40089 COG0478

40089 - COG0478

GO Terms:

GO:0005554

CD Domains:

Go To Gene Page:

40089
40341 WD40 superfamily

40341 - WD40 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

40341
7265 PIN_SF superfamily

7265 - PIN_SF superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

7265
GO ID Go Term p-value q-value Cluster
GO:0006177 GMP biosynthesis 0.00165341 1 Thaps_bicluster_0257
GO:0006468 protein amino acid phosphorylation 0.164893 1 Thaps_bicluster_0257
GO:0006508 proteolysis and peptidolysis 0.217787 1 Thaps_bicluster_0257
GO:0007046 ribosome biogenesis 0.00330476 1 Thaps_bicluster_0257
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