Thaps_bicluster_0214 Residual: 0.34
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_0214 0.34 Thalassiosira pseudonana
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Displaying 1 - 19 of 19
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10767 hypothetical protein

10767 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10767
20812 hypothetical protein

20812 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20812
22527 FNR_like

22527 - FNR_like

GO Terms:

GO:0006118, GO:0016491

CD Domains:

Go To Gene Page:

22527
2484 hypothetical protein

2484 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2484
24876 hypothetical protein

24876 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24876
25744 hypothetical protein

25744 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25744
261499 MttA_Hcf106 superfamily

261499 - MttA_Hcf106 superfamily

GO Terms:

GO:0008565, GO:0015031, GO:0009306, GO:0015450, GO:0016020

CD Domains:

Go To Gene Page:

261499
264921 (lhcx1) Chloroa_b-bind

264921 - (lhcx1) Chloroa_b-bind

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

264921
28443 (RL10) Ribosomal_L16_L10e

28443 - (RL10) Ribosomal_L16_L10e

GO Terms:

GO:0003735, GO:0005622, GO:0005840, GO:0006412

CD Domains:

Go To Gene Page:

28443
31216 AAT_I superfamily

31216 - AAT_I superfamily

GO Terms:

GO:0009058, GO:0016769, GO:0008710

CD Domains:

Go To Gene Page:

31216
32845 SDR_a5

32845 - SDR_a5

GO Terms:

NA

CD Domains:

Go To Gene Page:

32845
34543 (PPC2) PEPcase superfamily

34543 - (PPC2) PEPcase superfamily

GO Terms:

GO:0006099, GO:0008964

CD Domains:

Go To Gene Page:

34543
37359 (CLPP6) S14_ClpP_2

37359 - (CLPP6) S14_ClpP_2

GO Terms:

GO:0006508, GO:0008462

CD Domains:

Go To Gene Page:

37359
38879 (Lhcx2) Chloroa_b-bind

38879 - (Lhcx2) Chloroa_b-bind

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

38879
39841 ArsA_ATPase

39841 - ArsA_ATPase

GO Terms:

GO:0005524, GO:0006820, GO:0016020, GO:0015446, GO:0042961

CD Domains:

Go To Gene Page:

39841
8064 hypothetical protein

8064 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8064
ThpsCp022 (psaE) photosystem I subunit IV

ThpsCp022 - (psaE) photosystem I subunit IV

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp022
ThpsCp056 (psbZ) photosystem II protein Z

ThpsCp056 - (psbZ) photosystem II protein Z

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp056
ThpsCp076 (psbY) photosystem II protein Y

ThpsCp076 - (psbY) photosystem II protein Y

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp076
GO ID Go Term p-value q-value Cluster
GO:0009765 photosynthesis light harvesting 0.00287776 1 Thaps_bicluster_0214
GO:0009306 protein secretion 0.00824653 1 Thaps_bicluster_0214
GO:0006820 anion transport 0.0164318 1 Thaps_bicluster_0214
GO:0006099 tricarboxylic acid cycle 0.0205016 1 Thaps_bicluster_0214
GO:0015031 protein transport 0.0855012 1 Thaps_bicluster_0214
GO:0009058 biosynthesis 0.108157 1 Thaps_bicluster_0214
GO:0006412 protein biosynthesis 0.294992 1 Thaps_bicluster_0214
GO:0006118 electron transport 0.432304 1 Thaps_bicluster_0214
GO:0006508 proteolysis and peptidolysis 0.459068 1 Thaps_bicluster_0214
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