Thaps_bicluster_0079 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_0079 0.38 Thalassiosira pseudonana
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Displaying 1 - 23 of 23
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10548 hypothetical protein

10548 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10548
2018 HA

2018 - HA

GO Terms:

NA

CD Domains:

Go To Gene Page:

2018
20689 hypothetical protein

20689 - hypothetical protein

GO Terms:

GO:0016706, GO:0019538

CD Domains:

Go To Gene Page:

20689
21039 hypothetical protein

21039 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21039
2137 JmjC

2137 - JmjC

GO Terms:

GO:0005634

CD Domains:

Go To Gene Page:

2137
22622 CCT

22622 - CCT

GO Terms:

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:

22622
23199 WD40 superfamily

23199 - WD40 superfamily

GO Terms:

GO:0003677, GO:0005677, GO:0006342, GO:0006355

CD Domains:

Go To Gene Page:

23199
23494 hypothetical protein

23494 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23494
23513 COG1258

23513 - COG1258

GO Terms:

GO:0005215, GO:0006810

CD Domains:

Go To Gene Page:

23513
24323 RNase_PH superfamily

24323 - RNase_PH superfamily

GO Terms:

GO:0000175, GO:0003723, GO:0006396, GO:0004534, GO:0016896

CD Domains:

Go To Gene Page:

24323
24785 BTB superfamily

24785 - BTB superfamily

GO Terms:

GO:0005515, GO:0005249, GO:0006813, GO:0008076, GO:0016020

CD Domains:

Go To Gene Page:

24785
24877 hypothetical protein

24877 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24877
25640 hypothetical protein

25640 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25640
261017 Methyltransf_2 superfamily

261017 - Methyltransf_2 superfamily

GO Terms:

GO:0008757, GO:0008168

CD Domains:

Go To Gene Page:

261017
263650 NAD_binding_8 superfamily

263650 - NAD_binding_8 superfamily

GO Terms:

GO:0006118, GO:0008152, GO:0016491

CD Domains:

Go To Gene Page:

263650
264858 NAD_binding_8 superfamily

264858 - NAD_binding_8 superfamily

GO Terms:

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

CD Domains:

Go To Gene Page:

264858
29144 PRK06349

29144 - PRK06349

GO Terms:

GO:0004412, GO:0008652

CD Domains:

Go To Gene Page:

29144
39740 eIF-5_eIF-2B superfamily

39740 - eIF-5_eIF-2B superfamily

GO Terms:

GO:0003743, GO:0006413, GO:0006446

CD Domains:

Go To Gene Page:

39740
5797 ThTPase

5797 - ThTPase

GO Terms:

GO:0004016, GO:0006171, GO:0050333

CD Domains:

Go To Gene Page:

5797
6379 hypothetical protein

6379 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6379
8680 PseudoU_synth_RluCD_like

8680 - PseudoU_synth_RluCD_like

GO Terms:

GO:0003723, GO:0006396, GO:0009982, GO:0004730

CD Domains:

Go To Gene Page:

8680
900 POP1 superfamily

900 - POP1 superfamily

GO Terms:

GO:0001682, GO:0004526

CD Domains:

Go To Gene Page:

900
GO ID Go Term p-value q-value Cluster
GO:0006171 cAMP biosynthesis 0.00351458 1 Thaps_bicluster_0079
GO:0001682 tRNA 5'-leader removal 0.00351458 1 Thaps_bicluster_0079
GO:0006446 regulation of translational initiation 0.00701752 1 Thaps_bicluster_0079
GO:0006396 RNA processing 0.0171229 1 Thaps_bicluster_0079
GO:0006342 chromatin silencing 0.0312156 1 Thaps_bicluster_0079
GO:0008652 amino acid biosynthesis 0.0380267 1 Thaps_bicluster_0079
GO:0006813 potassium ion transport 0.0746894 1 Thaps_bicluster_0079
GO:0006725 aromatic compound metabolism 0.0746894 1 Thaps_bicluster_0079
GO:0006413 translational initiation 0.0812124 1 Thaps_bicluster_0079
GO:0019538 protein metabolism 0.150166 1 Thaps_bicluster_0079
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