Thaps_bicluster_0259 Residual: 0.35
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_0259 0.35 Thalassiosira pseudonana
Displaying 1 - 24 of 24
10252 hypothetical protein

10252 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10252
11147 HP_PGM_like

11147 - HP_PGM_like

GO Terms:

GO:0003824, GO:0008152

CD Domains:

Go To Gene Page:

11147
11172 hypothetical protein

11172 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11172
21908 hypothetical protein

21908 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21908
21925 NADB_Rossmann superfamily

21925 - NADB_Rossmann superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21925
2200 hypothetical protein

2200 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2200
22261 hypothetical protein

22261 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22261
22854 PTS_2-RNA

22854 - PTS_2-RNA

GO Terms:

GO:0006388, GO:0016772

CD Domains:

Go To Gene Page:

22854
24879 hypothetical protein

24879 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24879
25138 Methyltransf_32

25138 - Methyltransf_32

GO Terms:

GO:0008757

CD Domains:

Go To Gene Page:

25138
25359 hypothetical protein

25359 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25359
25730 Rdx superfamily

25730 - Rdx superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

25730
25800 hypothetical protein

25800 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25800
268449 Thioredoxin_like superfamily

268449 - Thioredoxin_like superfamily

GO Terms:

GO:0004364

CD Domains:

Go To Gene Page:

268449
270004 hypothetical protein

270004 - hypothetical protein

GO Terms:

GO:0005489, GO:0006118

CD Domains:

Go To Gene Page:

270004
2890 hypothetical protein

2890 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2890
32766 COG1936

32766 - COG1936

GO Terms:

NA

CD Domains:

Go To Gene Page:

32766
38646 TRX_family

38646 - TRX_family

GO Terms:

GO:0005489, GO:0006118, GO:0004791

CD Domains:

Go To Gene Page:

38646
38679 UBQ superfamily

38679 - UBQ superfamily

GO Terms:

GO:0006464

CD Domains:

Go To Gene Page:

38679
39698 Zn-ribbon_RPA12

39698 - Zn-ribbon_RPA12

GO Terms:

GO:0003677, GO:0003700, GO:0006354, GO:0006355, GO:0003899, GO:0003900, GO:0003901, GO:0003902

CD Domains:

Go To Gene Page:

39698
42412 RNAP_I_II_AC40

42412 - RNAP_I_II_AC40

GO Terms:

GO:0003677, GO:0003899, GO:0005634, GO:0006350, GO:0046983, GO:0003900, GO:0003901, GO:0003902

CD Domains:

Go To Gene Page:

42412
5806 TIM_phosphate_binding superfamily

5806 - TIM_phosphate_binding superfamily

GO Terms:

GO:0004425, GO:0006568

CD Domains:

Go To Gene Page:

5806
6380 hypothetical protein

6380 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6380
7031 CIA30 superfamily

7031 - CIA30 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

7031
GO ID Go Term p-value q-value Cluster
GO:0006388 tRNA splicing 0.00186066 1 Thaps_bicluster_0259
GO:0006354 RNA elongation 0.00742418 1 Thaps_bicluster_0259
GO:0006568 tryptophan metabolism 0.0111179 1 Thaps_bicluster_0259
GO:0006350 transcription 0.0544987 1 Thaps_bicluster_0259
GO:0006118 electron transport 0.0839917 1 Thaps_bicluster_0259
GO:0006464 protein modification 0.104655 1 Thaps_bicluster_0259
GO:0006355 regulation of transcription, DNA-dependent 0.446038 1 Thaps_bicluster_0259
GO:0008152 metabolism 0.546944 1 Thaps_bicluster_0259
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