Thaps_bicluster_0163 Residual: 0.38
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_0163 0.38 Thalassiosira pseudonana
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Displaying 1 - 26 of 26
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11733 hypothetical protein

11733 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11733
16193 S49_Sppa_N_C

16193 - S49_Sppa_N_C

GO Terms:

GO:0006508, GO:0008233

CD Domains:

Go To Gene Page:

16193
17695 SDR_c

17695 - SDR_c

GO Terms:

GO:0008152, GO:0016491, GO:0051341

CD Domains:

Go To Gene Page:

17695
1909 plant like protein

1909 - plant like protein

GO Terms:

GO:0005509

CD Domains:

Go To Gene Page:

1909
1959 hypothetical protein

1959 - hypothetical protein

GO Terms:

GO:0005198, GO:0003677, GO:0005634, GO:0006355

CD Domains:

Go To Gene Page:

1959
19639 Got1 superfamily

19639 - Got1 superfamily

GO Terms:

GO:0016192

CD Domains:

Go To Gene Page:

19639
21295 YCII superfamily

21295 - YCII superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21295
21327 DUF1625 superfamily

21327 - DUF1625 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21327
21617 Glyco_transf_15 superfamily

21617 - Glyco_transf_15 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21617
22246 hypothetical protein

22246 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22246
22714 hypothetical protein

22714 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22714
23278 GrpE

23278 - GrpE

GO Terms:

GO:0000774, GO:0006457, GO:0042803, GO:0051087

CD Domains:

Go To Gene Page:

23278
23929 hypothetical protein

23929 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23929
25156 hypothetical protein

25156 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25156
261882 Thioredoxin_like superfamily

261882 - Thioredoxin_like superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

261882
262963 HMPP_kinase

262963 - HMPP_kinase

GO Terms:

GO:0004807, GO:0008152, GO:0004152, GO:0006207, GO:0004789, GO:0009228

CD Domains:

Go To Gene Page:

262963
264008 AdoMet_MTases superfamily

264008 - AdoMet_MTases superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

264008
268324 60KD_IMP

268324 - 60KD_IMP

GO Terms:

GO:0016021, GO:0051205

CD Domains:

Go To Gene Page:

268324
270227 hypothetical protein

270227 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270227
2779 DmpA_OAT superfamily

2779 - DmpA_OAT superfamily

GO Terms:

GO:0004358, GO:0006526

CD Domains:

Go To Gene Page:

2779
3126 plant_peroxidase_like superfamily

3126 - plant_peroxidase_like superfamily

GO Terms:

GO:0004601, GO:0006979, GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

3126
3233 Thioredoxin_like superfamily

3233 - Thioredoxin_like superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

3233
35830 PgsA

35830 - PgsA

GO Terms:

GO:0008654, GO:0003881

CD Domains:

Go To Gene Page:

35830
43120 PDI_a_family

43120 - PDI_a_family

GO Terms:

GO:0005489, GO:0006118, GO:0003756

CD Domains:

Go To Gene Page:

43120
5314 hypothetical protein

5314 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5314
8073 TauD

8073 - TauD

GO Terms:

NA

CD Domains:

Go To Gene Page:

8073
GO ID Go Term p-value q-value Cluster
GO:0009228 thiamin biosynthesis 0.0123506 1 Thaps_bicluster_0163
GO:0051205 protein insertion into membrane 0.0123506 1 Thaps_bicluster_0163
GO:0006207 'de novo' pyrimidine base biosynthesis 0.0154159 1 Thaps_bicluster_0163
GO:0006526 arginine biosynthesis 0.0275887 1 Thaps_bicluster_0163
GO:0008654 phospholipid biosynthesis 0.0426071 1 Thaps_bicluster_0163
GO:0016192 vesicle-mediated transport 0.0485536 1 Thaps_bicluster_0163
GO:0051341 regulation of oxidoreductase activity 0.0690961 1 Thaps_bicluster_0163
GO:0006979 response to oxidative stress 0.0719967 1 Thaps_bicluster_0163
GO:0008152 metabolism 0.126308 1 Thaps_bicluster_0163
GO:0006457 protein folding 0.335858 1 Thaps_bicluster_0163
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