Thaps_bicluster_0260 Residual: 0.25
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_0260 0.25 Thalassiosira pseudonana
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Displaying 1 - 19 of 19
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10233 COG1233

10233 - COG1233

GO Terms:

GO:0006118, GO:0016491, GO:0015036, GO:0016117, GO:0016705, GO:0050660

CD Domains:

Go To Gene Page:

10233
10809 hypothetical protein

10809 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10809
11757 hypothetical protein

11757 - hypothetical protein

GO Terms:

GO:0005509

CD Domains:

Go To Gene Page:

11757
1449 hypothetical protein

1449 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1449
22744 hypothetical protein

22744 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22744
2352 ClpS

2352 - ClpS

GO Terms:

NA

CD Domains:

Go To Gene Page:

2352
261390 NAD_binding_8 superfamily

261390 - NAD_binding_8 superfamily

GO Terms:

GO:0004497, GO:0006725, GO:0006118, GO:0008152, GO:0016491, GO:0018658

CD Domains:

Go To Gene Page:

261390
263658 GUN4

263658 - GUN4

GO Terms:

NA

CD Domains:

Go To Gene Page:

263658
268474 PLN02657

268474 - PLN02657

GO Terms:

GO:0003824, GO:0016628, GO:0016631, GO:0018498, GO:0018499, GO:0018500, GO:0018501, GO:0018502, GO:0018503

CD Domains:

Go To Gene Page:

268474
268480 (GGPS1) Trans_IPPS_HT

268480 - (GGPS1) Trans_IPPS_HT

GO Terms:

GO:0008299

CD Domains:

Go To Gene Page:

268480
270346 hypothetical protein

270346 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

270346
31012 (Cpx1) PLN02873

31012 - (Cpx1) PLN02873

GO Terms:

GO:0004109, GO:0006779

CD Domains:

Go To Gene Page:

31012
3326 TauD

3326 - TauD

GO Terms:

NA

CD Domains:

Go To Gene Page:

3326
37534 MRP-like

37534 - MRP-like

GO Terms:

GO:0005524, GO:0005554

CD Domains:

Go To Gene Page:

37534
38807 KDPG_aldolase

38807 - KDPG_aldolase

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

38807
8248 HopJ superfamily

8248 - HopJ superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

8248
8912 hypothetical protein

8912 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8912
9021 (PbgD) hemC

9021 - (PbgD) hemC

GO Terms:

GO:0004418, GO:0006779

CD Domains:

Go To Gene Page:

9021
9352 LrgB superfamily

9352 - LrgB superfamily

GO Terms:

GO:0016020

CD Domains:

Go To Gene Page:

9352
GO ID Go Term p-value q-value Cluster
GO:0006779 porphyrin biosynthesis 0.000306536 0.83623 Thaps_bicluster_0260
GO:0015969 guanosine tetraphosphate metabolic process 0.00248088 1 Thaps_bicluster_0260
GO:0008152 metabolism 0.267706 1 Thaps_bicluster_0260
GO:0016117 carotenoid biosynthesis 0.0196897 1 Thaps_bicluster_0260
GO:0008299 isoprenoid biosynthesis 0.0269812 1 Thaps_bicluster_0260
GO:0006725 aromatic compound metabolism 0.0532936 1 Thaps_bicluster_0260
GO:0006260 DNA replication 0.0835483 1 Thaps_bicluster_0260
GO:0006118 electron transport 0.138361 1 Thaps_bicluster_0260
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