Thaps_bicluster_0203 Residual: 0.30
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_0203 0.30 Thalassiosira pseudonana
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Displaying 1 - 23 of 23
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10092 hypothetical protein

10092 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10092
11086 hypothetical protein

11086 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11086
11171 hypothetical protein

11171 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11171
11822 hypothetical protein

11822 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11822
20024 FKBP_C

20024 - FKBP_C

GO Terms:

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

CD Domains:

Go To Gene Page:

20024
20593 FA_hydroxylase

20593 - FA_hydroxylase

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

20593
21348 hypothetical protein

21348 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21348
22362 (KCS1) CHS_like

22362 - (KCS1) CHS_like

GO Terms:

GO:0008415, GO:0009058, GO:0016210

CD Domains:

Go To Gene Page:

22362
23292 Membrane-FADS-like superfamily

23292 - Membrane-FADS-like superfamily

GO Terms:

GO:0016491

CD Domains:

Go To Gene Page:

23292
23357 PLN02779

23357 - PLN02779

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

23357
25544 (PGP) PLN02645

25544 - (PGP) PLN02645

GO Terms:

GO:0003824, GO:0008152, GO:0016791, GO:0016787, GO:0003869

CD Domains:

Go To Gene Page:

25544
261275 ThylakoidFormat superfamily

261275 - ThylakoidFormat superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

261275
261407 NAD_binding_8 superfamily
270213 (Hlip2) high light induced protein 2

270213 - (Hlip2) high light induced protein 2

GO Terms:

NA

CD Domains:

Go To Gene Page:

270213
270357 hypothetical protein

270357 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270357
37288 PLN02487

37288 - PLN02487

GO Terms:

GO:0006118, GO:0016491, GO:0016719

CD Domains:

Go To Gene Page:

37288
3748 Mito_carr

3748 - Mito_carr

GO Terms:

GO:0005488, GO:0006810, GO:0016020, GO:0005743

CD Domains:

Go To Gene Page:

3748
38221 bPH_2

38221 - bPH_2

GO Terms:

NA

CD Domains:

Go To Gene Page:

38221
41113 (DES3) PLN03199

41113 - (DES3) PLN03199

GO Terms:

GO:0016491, GO:0006636, GO:0016020, GO:0016717

CD Domains:

Go To Gene Page:

41113
4379 RAP

4379 - RAP

GO Terms:

NA

CD Domains:

Go To Gene Page:

4379
4382 DUF2854 superfamily

4382 - DUF2854 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

4382
5380 DUF1092 superfamily

5380 - DUF1092 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

5380
6857 hypothetical protein

6857 - hypothetical protein

GO Terms:

GO:0016021

CD Domains:

Go To Gene Page:

6857
GO ID Go Term p-value q-value Cluster
GO:0008152 metabolism 0.010109 1 Thaps_bicluster_0203
GO:0016117 carotenoid biosynthesis 0.0180619 1 Thaps_bicluster_0203
GO:0006636 fatty acid desaturation 0.0269812 1 Thaps_bicluster_0203
GO:0009058 biosynthesis 0.118319 1 Thaps_bicluster_0203
GO:0006118 electron transport 0.119465 1 Thaps_bicluster_0203
GO:0006457 protein folding 0.25918 1 Thaps_bicluster_0203
GO:0006810 transport 0.347574 1 Thaps_bicluster_0203
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