Thaps_bicluster_0186 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_0186 0.38 Thalassiosira pseudonana
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Displaying 1 - 22 of 22
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10271 hypothetical protein

10271 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10271
12943 NARP1

12943 - NARP1

GO Terms:

GO:0004596

CD Domains:

Go To Gene Page:

12943
15688 MFS

15688 - MFS

GO Terms:

GO:0005215, GO:0006810, GO:0016021

CD Domains:

Go To Gene Page:

15688
22750 hypothetical protein

22750 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22750
23106 hypothetical protein

23106 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23106
23472 hypothetical protein

23472 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23472
24140 hypothetical protein

24140 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24140
24632 PDCD2_C superfamily

24632 - PDCD2_C superfamily

GO Terms:

GO:0003910, GO:0005524, GO:0006260, GO:0006281, GO:0006310

CD Domains:

Go To Gene Page:

24632
2609 WD40 superfamily

2609 - WD40 superfamily

GO Terms:

GO:0003677, GO:0005634

CD Domains:

Go To Gene Page:

2609
261250 Phytochelatin

261250 - Phytochelatin

GO Terms:

NA

CD Domains:

Go To Gene Page:

261250
262343 LacZ

262343 - LacZ

GO Terms:

GO:0004197, GO:0006508

CD Domains:

Go To Gene Page:

262343
262400 ANK

262400 - ANK

GO Terms:

NA

CD Domains:

Go To Gene Page:

262400
3017 SNARE_assoc

3017 - SNARE_assoc

GO Terms:

NA

CD Domains:

Go To Gene Page:

3017
34710 SNF2_N

34710 - SNF2_N

GO Terms:

GO:0003677, GO:0005524, GO:0003676, GO:0004386

CD Domains:

Go To Gene Page:

34710
36345 (Tp_sigma70.3b) Sig70-cyanoRpoD

36345 - (Tp_sigma70.3b) Sig70-cyanoRpoD

GO Terms:

GO:0003677, GO:0003700, GO:0006352, GO:0006355, GO:0016987, GO:0005524

CD Domains:

Go To Gene Page:

36345
36501 UBCc superfamily

36501 - UBCc superfamily

GO Terms:

GO:0004840, GO:0006464, GO:0006512, GO:0004842

CD Domains:

Go To Gene Page:

36501
38475 HA2

38475 - HA2

GO Terms:

GO:0005524, GO:0008026, GO:0004386

CD Domains:

Go To Gene Page:

38475
38757 trmE

38757 - trmE

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

38757
5053 hypothetical protein

5053 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5053
6255 hypothetical protein

6255 - hypothetical protein

GO Terms:

GO:0016706, GO:0019538

CD Domains:

Go To Gene Page:

6255
8259 hypothetical protein

8259 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8259
GO ID Go Term p-value q-value Cluster
GO:0006352 transcription initiation 0.0265779 1 Thaps_bicluster_0186
GO:0006310 DNA recombination 0.0386288 1 Thaps_bicluster_0186
GO:0006260 DNA replication 0.0701108 1 Thaps_bicluster_0186
GO:0006512 ubiquitin cycle 0.0720473 1 Thaps_bicluster_0186
GO:0019538 protein metabolism 0.0912132 1 Thaps_bicluster_0186
GO:0006281 DNA repair 0.0912132 1 Thaps_bicluster_0186
GO:0006464 protein modification 0.115596 1 Thaps_bicluster_0186
GO:0006810 transport 0.321719 1 Thaps_bicluster_0186
GO:0006508 proteolysis and peptidolysis 0.459068 1 Thaps_bicluster_0186
GO:0006355 regulation of transcription, DNA-dependent 0.481263 1 Thaps_bicluster_0186
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