Thaps_bicluster_0101 Residual: 0.32
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_0101 0.32 Thalassiosira pseudonana
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Displaying 1 - 22 of 22
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20469 PLN00032

20469 - PLN00032

GO Terms:

GO:0003899, GO:0006350, GO:0003900, GO:0003901, GO:0003902

CD Domains:

Go To Gene Page:

20469
22276 Gar1

22276 - Gar1

GO Terms:

GO:0006364, GO:0007046, GO:0019843, GO:0030532

CD Domains:

Go To Gene Page:

22276
23737 tRNA_m1G_MT superfamily

23737 - tRNA_m1G_MT superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

23737
24369 (Tp_CCCH1) RRM_SF superfamily

24369 - (Tp_CCCH1) RRM_SF superfamily

GO Terms:

GO:0003676, GO:0005215, GO:0006810

CD Domains:

Go To Gene Page:

24369
24904 PIN_SF superfamily

24904 - PIN_SF superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

24904
262775 RBFA

262775 - RBFA

GO Terms:

NA

CD Domains:

Go To Gene Page:

262775
263801 RluA

263801 - RluA

GO Terms:

GO:0003723, GO:0006396, GO:0009982, GO:0004730, GO:0016439

CD Domains:

Go To Gene Page:

263801
263845 RRM_SF superfamily

263845 - RRM_SF superfamily

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

263845
26686 WD40

26686 - WD40

GO Terms:

GO:0003847

CD Domains:

Go To Gene Page:

26686
268296 (RM12) Ribosomal_L7_L12

268296 - (RM12) Ribosomal_L7_L12

GO Terms:

GO:0003735, GO:0005622, GO:0005840, GO:0006412

CD Domains:

Go To Gene Page:

268296
268744 SUA5

268744 - SUA5

GO Terms:

GO:0005554

CD Domains:

Go To Gene Page:

268744
28570 (L7Ae) Ribosomal_L7Ae superfamily

28570 - (L7Ae) Ribosomal_L7Ae superfamily

GO Terms:

GO:0003735, GO:0005622, GO:0005840, GO:0006412, GO:0030529, GO:0042254

CD Domains:

Go To Gene Page:

28570
31047 Brix

31047 - Brix

GO Terms:

NA

CD Domains:

Go To Gene Page:

31047
33088 Obg_CgtA

33088 - Obg_CgtA

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

33088
33589 Brix superfamily

33589 - Brix superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

33589
33718 Methyltransf_4 superfamily

33718 - Methyltransf_4 superfamily

GO Terms:

GO:0008757, GO:0008176

CD Domains:

Go To Gene Page:

33718
34826 zf-C2H2_jaz superfamily

34826 - zf-C2H2_jaz superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

34826
40985 Nucleostemin_like

40985 - Nucleostemin_like

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

40985
41419 (RT4) RpsD

41419 - (RT4) RpsD

GO Terms:

GO:0003735, GO:0005622, GO:0005840, GO:0006412, GO:0003723

CD Domains:

Go To Gene Page:

41419
42594 Ribosomal_P0_like

42594 - Ribosomal_P0_like

GO Terms:

GO:0005622, GO:0042254

CD Domains:

Go To Gene Page:

42594
5906 hypothetical protein

5906 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5906
9442 PTZ00146

9442 - PTZ00146

GO Terms:

GO:0003723, GO:0005634, GO:0006364

CD Domains:

Go To Gene Page:

9442
GO ID Go Term p-value q-value Cluster
GO:0042254 ribosome biogenesis and assembly 0.0000981 0.269301 Thaps_bicluster_0101
GO:0006364 rRNA processing 0.000130693 0.358099 Thaps_bicluster_0101
GO:0006412 protein biosynthesis 0.00534523 1 Thaps_bicluster_0101
GO:0007046 ribosome biogenesis 0.00906837 1 Thaps_bicluster_0101
GO:0006350 transcription 0.0662137 1 Thaps_bicluster_0101
GO:0006396 RNA processing 0.124391 1 Thaps_bicluster_0101
GO:0006810 transport 0.347574 1 Thaps_bicluster_0101
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