Thaps_bicluster_0115 Residual: 0.37
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_0115 0.37 Thalassiosira pseudonana
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Displaying 1 - 25 of 25
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1460 hypothetical protein

1460 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1460
19626 ZnMc superfamily

19626 - ZnMc superfamily

GO Terms:

GO:0006508, GO:0008533

CD Domains:

Go To Gene Page:

19626
19895 BTB

19895 - BTB

GO Terms:

GO:0005515

CD Domains:

Go To Gene Page:

19895
21400 hypothetical protein

21400 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21400
21983 hypothetical protein

21983 - hypothetical protein

GO Terms:

GO:0004339

CD Domains:

Go To Gene Page:

21983
22908 hypothetical protein

22908 - hypothetical protein

GO Terms:

GO:0005576, GO:0006030, GO:0008061

CD Domains:

Go To Gene Page:

22908
23486 LRR_RI superfamily

23486 - LRR_RI superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

23486
23700 lysozyme_like superfamily

23700 - lysozyme_like superfamily

GO Terms:

GO:0004568, GO:0006032, GO:0009613, GO:0016998, GO:0016020, GO:0030154

CD Domains:

Go To Gene Page:

23700
24000 DENN superfamily

24000 - DENN superfamily

GO Terms:

GO:0005524, GO:0006810, GO:0016020, GO:0042626

CD Domains:

Go To Gene Page:

24000
24026 hypothetical protein

24026 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24026
24415 hypothetical protein

24415 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24415
24434 hypothetical protein

24434 - hypothetical protein

GO Terms:

GO:0005179, GO:0005576, GO:0000151, GO:0004842, GO:0008270, GO:0016567, GO:0004308

CD Domains:

Go To Gene Page:

24434
25067 hypothetical protein

25067 - hypothetical protein

GO Terms:

GO:0004402

CD Domains:

Go To Gene Page:

25067
25080 hypothetical protein

25080 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25080
25137 hypothetical protein

25137 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25137
25781 hypothetical protein

25781 - hypothetical protein

GO Terms:

GO:0004339

CD Domains:

Go To Gene Page:

25781
25782 hypothetical protein

25782 - hypothetical protein

GO Terms:

GO:0003824, 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:

25782
260958 PLN02895

260958 - PLN02895

GO Terms:

GO:0005975, GO:0016868, GO:0004610

CD Domains:

Go To Gene Page:

260958
264357 ZntA
268366 Glyco_18

268366 - Glyco_18

GO Terms:

GO:0008152, GO:0016787, GO:0004568, GO:0008843

CD Domains:

Go To Gene Page:

268366
268614 PseudoU_synth superfamily

268614 - PseudoU_synth superfamily

GO Terms:

GO:0009982, GO:0016439

CD Domains:

Go To Gene Page:

268614
269725 PLN00113

269725 - PLN00113

GO Terms:

NA

CD Domains:

Go To Gene Page:

269725
31762 (CAT2) Carn_acyltransf superfamily

31762 - (CAT2) Carn_acyltransf superfamily

GO Terms:

GO:0008415, GO:0004092

CD Domains:

Go To Gene Page:

31762
37041 NagA

37041 - NagA

GO Terms:

GO:0016787, GO:0008448

CD Domains:

Go To Gene Page:

37041
4146 hypothetical protein

4146 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4146
GO ID Go Term p-value q-value Cluster
GO:0030154 cell differentiation 0.00289436 1 Thaps_bicluster_0115
GO:0006032 chitin catabolism 0.0229381 1 Thaps_bicluster_0115
GO:0016998 cell wall catabolism 0.0257707 1 Thaps_bicluster_0115
GO:0009613 response to pest, pathogen or parasite 0.0257707 1 Thaps_bicluster_0115
GO:0030001 metal ion transport 0.0370252 1 Thaps_bicluster_0115
GO:0015992 proton transport 0.0426071 1 Thaps_bicluster_0115
GO:0006030 chitin metabolism 0.059173 1 Thaps_bicluster_0115
GO:0006812 cation transport 0.117664 1 Thaps_bicluster_0115
GO:0005975 carbohydrate metabolism 0.196738 1 Thaps_bicluster_0115
GO:0016567 protein ubiquitination 0.206145 1 Thaps_bicluster_0115
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