Thaps_bicluster_0159 Residual: 0.26
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_0159 0.26 Thalassiosira pseudonana
Displaying 1 - 20 of 20
10360 (Tp_bZIP24a) regulator [Rayko]

10360 - (Tp_bZIP24a) regulator [Rayko]

GO Terms:

GO:0003677, GO:0005634, GO:0006355

CD Domains:

Go To Gene Page:

10360
22208 COG0075

22208 - COG0075

GO Terms:

GO:0008453

CD Domains:

Go To Gene Page:

22208
22396 hypothetical protein

22396 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22396
233 CdCA1

233 - CdCA1

GO Terms:

NA

CD Domains:

Go To Gene Page:

233
260953 COG2423

260953 - COG2423

GO Terms:

NA

CD Domains:

Go To Gene Page:

260953
263924 MFS

263924 - MFS

GO Terms:

GO:0005215, GO:0006810, GO:0016021

CD Domains:

Go To Gene Page:

263924
264181 hypothetical protein

264181 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

264181
269696 hypothetical protein

269696 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

269696
269942 SHMT

269942 - SHMT

GO Terms:

GO:0004372, GO:0006544, GO:0006563

CD Domains:

Go To Gene Page:

269942
28521 (GDCH) GCS_H

28521 - (GDCH) GCS_H

GO Terms:

GO:0005960, GO:0006546, GO:0004047, GO:0004374

CD Domains:

Go To Gene Page:

28521
34125 CdCA1

34125 - CdCA1

GO Terms:

NA

CD Domains:

Go To Gene Page:

34125
36208 (GDCT) PLN02319

36208 - (GDCT) PLN02319

GO Terms:

GO:0004047, GO:0005737, GO:0006546, GO:0004374

CD Domains:

Go To Gene Page:

36208
3974 (UroD2) URO-D

3974 - (UroD2) URO-D

GO Terms:

GO:0004853, GO:0006779

CD Domains:

Go To Gene Page:

3974
39799 (GDCP) PLN02414

39799 - (GDCP) PLN02414

GO Terms:

GO:0005509, GO:0004375, GO:0005961, GO:0006544, GO:0004374

CD Domains:

Go To Gene Page:

39799
412 (ALAT_1) PTZ00377

412 - (ALAT_1) PTZ00377

GO Terms:

GO:0009058, GO:0016847, GO:0016769, GO:0004021

CD Domains:

Go To Gene Page:

412
4819 Bestrophin superfamily

4819 - Bestrophin superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

4819
4820 Bestrophin superfamily

4820 - Bestrophin superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

4820
6528 hypothetical protein

6528 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6528
6529 hypothetical protein

6529 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6529
9903 (Tp_bZIP24b) regulator [Rayko]

9903 - (Tp_bZIP24b) regulator [Rayko]

GO Terms:

GO:0003677, GO:0005634, GO:0006355

CD Domains:

Go To Gene Page:

9903
GO ID Go Term p-value q-value Cluster
GO:0006544 glycine metabolism 0.000023 0.0634592 Thaps_bicluster_0159
GO:0006546 glycine catabolism 0.0000383 0.105534 Thaps_bicluster_0159
GO:0006563 L-serine metabolism 0.00619065 1 Thaps_bicluster_0159
GO:0006779 porphyrin biosynthesis 0.0225308 1 Thaps_bicluster_0159
GO:0009058 biosynthesis 0.108157 1 Thaps_bicluster_0159
GO:0006355 regulation of transcription, DNA-dependent 0.129013 1 Thaps_bicluster_0159
GO:0006810 transport 0.321719 1 Thaps_bicluster_0159
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