Thaps_bicluster_0224 Residual: 0.27
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_0224 0.27 Thalassiosira pseudonana
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 20 of 20
" class="views-fluidgrid-wrapper clear-block">
11737 hypothetical protein

11737 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11737
1961 NAD_binding_8 superfamily

1961 - NAD_binding_8 superfamily

GO Terms:

GO:0004497, GO:0006725, GO:0006118, GO:0008152, GO:0016491

CD Domains:

Go To Gene Page:

1961
261608 PLN02585

261608 - PLN02585

GO Terms:

GO:0008757, GO:0015979, GO:0015995, GO:0046406

CD Domains:

Go To Gene Page:

261608
262279 PT_UbiA_chlorophyll

262279 - PT_UbiA_chlorophyll

GO Terms:

GO:0004659, GO:0016021, GO:0030494

CD Domains:

Go To Gene Page:

262279
262313 Chloroa_b-bind superfamily

262313 - Chloroa_b-bind superfamily

GO Terms:

GO:0009765, GO:0016020, GO:0004601, GO:0006979

CD Domains:

Go To Gene Page:

262313
268192 Zip superfamily

268192 - Zip superfamily

GO Terms:

GO:0016020, GO:0030001, GO:0046873

CD Domains:

Go To Gene Page:

268192
270287 hypothetical protein

270287 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270287
32375 Zip superfamily

32375 - Zip superfamily

GO Terms:

GO:0016020, GO:0030001, GO:0046873

CD Domains:

Go To Gene Page:

32375
32723 Chloroa_b-bind

32723 - Chloroa_b-bind

GO Terms:

GO:0009765, GO:0016020

CD Domains:

Go To Gene Page:

32723
3581 hypothetical protein

3581 - hypothetical protein

GO Terms:

GO:0006457

CD Domains:

Go To Gene Page:

3581
36243 cyclophilin superfamily

36243 - cyclophilin superfamily

GO Terms:

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

CD Domains:

Go To Gene Page:

36243
37338 Thioredoxin_like superfamily

37338 - Thioredoxin_like superfamily

GO Terms:

GO:0005489, GO:0006118, GO:0003756

CD Domains:

Go To Gene Page:

37338
38724 plant_peroxidase_like superfamily

38724 - plant_peroxidase_like superfamily

GO Terms:

GO:0004601, GO:0006979, GO:0016688

CD Domains:

Go To Gene Page:

38724
4002 Peptidase_M14_like superfamily

4002 - Peptidase_M14_like superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

4002
4976 Abhydrolase_6

4976 - Abhydrolase_6

GO Terms:

GO:0003824

CD Domains:

Go To Gene Page:

4976
5415 Thioredoxin_like superfamily

5415 - Thioredoxin_like superfamily

GO Terms:

GO:0005489, GO:0006118, GO:0045454

CD Domains:

Go To Gene Page:

5415
7060 hypothetical protein

7060 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7060
7510 hypothetical protein

7510 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7510
7906 CreA superfamily

7906 - CreA superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

7906
9467 hypothetical protein

9467 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9467
GO ID Go Term p-value q-value Cluster
GO:0030001 metal ion transport 0.000886575 1 Thaps_bicluster_0224
GO:0006979 response to oxidative stress 0.00306659 1 Thaps_bicluster_0224
GO:0030494 bacteriochlorophyll biosynthesis 0.00351458 1 Thaps_bicluster_0224
GO:0009765 photosynthesis light harvesting 0.00838496 1 Thaps_bicluster_0224
GO:0015995 chlorophyll biosynthesis 0.0139887 1 Thaps_bicluster_0224
GO:0045454 cell redox homeostasis 0.0312156 1 Thaps_bicluster_0224
GO:0015979 photosynthesis 0.0447927 1 Thaps_bicluster_0224
GO:0006118 electron transport 0.0631194 1 Thaps_bicluster_0224
GO:0006725 aromatic compound metabolism 0.0746894 1 Thaps_bicluster_0224
GO:0006457 protein folding 0.0749473 1 Thaps_bicluster_0224
Log in to post comments