Thaps_bicluster_0254 Residual: 0.29
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_0254 0.29 Thalassiosira pseudonana
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Displaying 1 - 23 of 23
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15976 PTZ00348

15976 - PTZ00348

GO Terms:

GO:0004812, GO:0005524, GO:0006418, GO:0004831

CD Domains:

Go To Gene Page:

15976
20930 DRE_TIM_metallolyase superfamily

20930 - DRE_TIM_metallolyase superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

20930
2094 Cyt_C5_DNA_methylase superfamily

2094 - Cyt_C5_DNA_methylase superfamily

GO Terms:

GO:0003677, GO:0006306

CD Domains:

Go To Gene Page:

2094
2128 hypothetical protein

2128 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2128
22840 hypothetical protein

22840 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22840
23442 hypothetical protein

23442 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23442
2452 DUF1244 superfamily

2452 - DUF1244 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

2452
25486 PseudoU_synth_RluCD_like

25486 - PseudoU_synth_RluCD_like

GO Terms:

NA

CD Domains:

Go To Gene Page:

25486
262303 (Helicase_2) UvrD-helicase

262303 - (Helicase_2) UvrD-helicase

GO Terms:

GO:0003677, GO:0004003, GO:0005524, GO:0006281, 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:

262303
263034 WD40-repeat protein

263034 - WD40-repeat protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

263034
263425 HP_PGM_like

263425 - HP_PGM_like

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

263425
268327 PseudoU_synth superfamily

268327 - PseudoU_synth superfamily

GO Terms:

GO:0009982, GO:0016439

CD Domains:

Go To Gene Page:

268327
269028 Methyltrans_RNA superfamily

269028 - Methyltrans_RNA superfamily

GO Terms:

GO:0005554

CD Domains:

Go To Gene Page:

269028
32996 (Tp_CCCH4) DUS_like_FMN

32996 - (Tp_CCCH4) DUS_like_FMN

GO Terms:

GO:0008033, GO:0016491, GO:0050660, GO:0051341

CD Domains:

Go To Gene Page:

32996
34412 Clp1 superfamily

34412 - Clp1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

34412
3580 ANK

3580 - ANK

GO Terms:

NA

CD Domains:

Go To Gene Page:

3580
37705 DUF4110

37705 - DUF4110

GO Terms:

NA

CD Domains:

Go To Gene Page:

37705
38391 hypothetical protein

38391 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

38391
38509 YihA_EngB

38509 - YihA_EngB

GO Terms:

GO:0005525

CD Domains:

Go To Gene Page:

38509
39924 (TopoII_1) gyrB

39924 - (TopoII_1) gyrB

GO Terms:

GO:0003677, GO:0003918, GO:0005524, GO:0006259, GO:0006265, GO:0003676, GO:0006304

CD Domains:

Go To Gene Page:

39924
4517 hypothetical protein

4517 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

4517
4947 PP-ATPase

4947 - PP-ATPase

GO Terms:

NA

CD Domains:

Go To Gene Page:

4947
5007 hypothetical protein

5007 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5007
GO ID Go Term p-value q-value Cluster
GO:0006304 DNA modification 0.00557274 1 Thaps_bicluster_0254
GO:0006265 DNA topological change 0.0184686 1 Thaps_bicluster_0254
GO:0006259 DNA metabolism 0.0257707 1 Thaps_bicluster_0254
GO:0008033 tRNA processing 0.0330245 1 Thaps_bicluster_0254
GO:0051341 regulation of oxidoreductase activity 0.0420242 1 Thaps_bicluster_0254
GO:0006306 DNA methylation 0.0527255 1 Thaps_bicluster_0254
GO:0006281 DNA repair 0.0824713 1 Thaps_bicluster_0254
GO:0006418 tRNA aminoacylation for protein translation 0.101273 1 Thaps_bicluster_0254
GO:0008152 metabolism 0.546944 1 Thaps_bicluster_0254
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