Thaps_bicluster_0195 Residual: 0.28
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_0195 0.28 Thalassiosira pseudonana
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Displaying 1 - 18 of 18
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1680 AdoMet_MTases superfamily

1680 - AdoMet_MTases superfamily

GO Terms:

GO:0008168

CD Domains:

Go To Gene Page:

1680
21524 Cupin_8 superfamily

21524 - Cupin_8 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21524
22482 hypothetical protein

22482 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22482
23751 TYW3 superfamily

23751 - TYW3 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

23751
25434 PRK00142

25434 - PRK00142

GO Terms:

NA

CD Domains:

Go To Gene Page:

25434
25824 hypothetical protein

25824 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25824
268455 hypothetical protein

268455 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268455
26931 GTP_cyclohydro1

26931 - GTP_cyclohydro1

GO Terms:

GO:0003934, GO:0009058

CD Domains:

Go To Gene Page:

26931
32325 ABC_ATPase superfamily

32325 - ABC_ATPase superfamily

GO Terms:

GO:0005524, GO:0016887, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

32325
32414 PRK00093

32414 - PRK00093

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

32414
37374 PseudoU_synth superfamily

37374 - PseudoU_synth superfamily

GO Terms:

GO:0004730, GO:0006396, GO:0008033

CD Domains:

Go To Gene Page:

37374
37786 SrmB

37786 - SrmB

GO Terms:

GO:0005524, GO:0008026, GO:0003676, GO:0004386

CD Domains:

Go To Gene Page:

37786
40884 (RPA1) RNAP_I_RPA1_N

40884 - (RPA1) RNAP_I_RPA1_N

GO Terms:

GO:0003677, GO:0003899, GO:0005634, GO:0006350, GO:0005524, GO:0003900, GO:0003901, GO:0003902

CD Domains:

Go To Gene Page:

40884
42821 PRK14333

42821 - PRK14333

GO Terms:

GO:0005554, GO:0003824, GO:0005506

CD Domains:

Go To Gene Page:

42821
5236 DUF819 superfamily

5236 - DUF819 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

5236
6842 DUF914

6842 - DUF914

GO Terms:

NA

CD Domains:

Go To Gene Page:

6842
9040 ELP3

9040 - ELP3

GO Terms:

GO:0008080, GO:0003824, GO:0005506, GO:0004402

CD Domains:

Go To Gene Page:

9040
GO ID Go Term p-value q-value Cluster
GO:0008033 tRNA processing 0.0148069 1 Thaps_bicluster_0195
GO:0006350 transcription 0.0245865 1 Thaps_bicluster_0195
GO:0009058 biosynthesis 0.0447265 1 Thaps_bicluster_0195
GO:0006396 RNA processing 0.0471222 1 Thaps_bicluster_0195
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