Thaps_bicluster_0238 Residual: 0.33
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_0238 0.33 Thalassiosira pseudonana
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Displaying 1 - 23 of 23
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11175 Mitofilin

11175 - Mitofilin

GO Terms:

NA

CD Domains:

Go To Gene Page:

11175
11572 hypothetical protein

11572 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11572
11615 PRK15061

11615 - PRK15061

GO Terms:

GO:0004096, GO:0004601, GO:0006118, GO:0006979, GO:0004130

CD Domains:

Go To Gene Page:

11615
2325 hypothetical protein

2325 - hypothetical protein

GO Terms:

GO:0008757, GO:0008168

CD Domains:

Go To Gene Page:

2325
262506 Phosphonate-bd superfamily

262506 - Phosphonate-bd superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

262506
263515 RimL

263515 - RimL

GO Terms:

NA

CD Domains:

Go To Gene Page:

263515
268541 (UBA1) Ube1

268541 - (UBA1) Ube1

GO Terms:

GO:0004839, GO:0006464, GO:0006512, GO:0003824, GO:0004842

CD Domains:

Go To Gene Page:

268541
28496 (AHC3) PRK05476

28496 - (AHC3) PRK05476

GO Terms:

GO:0004013, GO:0006730

CD Domains:

Go To Gene Page:

28496
30620 Cfa

30620 - Cfa

GO Terms:

GO:0008757, GO:0008610, GO:0008825

CD Domains:

Go To Gene Page:

30620
32321 TRX_family

32321 - TRX_family

GO Terms:

GO:0005489, GO:0006118, GO:0004791

CD Domains:

Go To Gene Page:

32321
33798 PKc_like superfamily

33798 - PKc_like superfamily

GO Terms:

GO:0004672, GO:0005524, GO:0006468, GO:0004713, GO:0004674

CD Domains:

Go To Gene Page:

33798
3448 Guanylate_kin

3448 - Guanylate_kin

GO Terms:

GO:0004384, GO:0004385

CD Domains:

Go To Gene Page:

3448
35816 (GAPD2) PRK08955

35816 - (GAPD2) PRK08955

GO Terms:

GO:0004365, GO:0006096, GO:0051287, GO:0006006, GO:0008943

CD Domains:

Go To Gene Page:

35816
36592 HMGB-UBF_HMG-box

36592 - HMGB-UBF_HMG-box

GO Terms:

GO:0000785, GO:0003677, GO:0005634, GO:0006355

CD Domains:

Go To Gene Page:

36592
37976 cyclophilin_ABH_like

37976 - cyclophilin_ABH_like

GO Terms:

GO:0006457, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

37976
38266 (GPI1) pgi

38266 - (GPI1) pgi

GO Terms:

GO:0004347, GO:0006094, GO:0006096

CD Domains:

Go To Gene Page:

38266
39299 (ARF3) Arf1_5_like

39299 - (ARF3) Arf1_5_like

GO Terms:

GO:0005525, GO:0007264, GO:0015031, GO:0006886

CD Domains:

Go To Gene Page:

39299
41291 (CAM1) PTZ00184

41291 - (CAM1) PTZ00184

GO Terms:

GO:0005509

CD Domains:

Go To Gene Page:

41291
43150 PolyPPase_VTC4_like

43150 - PolyPPase_VTC4_like

GO Terms:

NA

CD Domains:

Go To Gene Page:

43150
5954 PRK05476

5954 - PRK05476

GO Terms:

GO:0004013, GO:0006730

CD Domains:

Go To Gene Page:

5954
8524 pntA

8524 - pntA

GO Terms:

GO:0006118, GO:0008746, GO:0008750, GO:0015992, GO:0016491

CD Domains:

Go To Gene Page:

8524
8701 hypothetical protein

8701 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8701
9569 hypothetical protein

9569 - hypothetical protein

GO Terms:

GO:0004308

CD Domains:

Go To Gene Page:

9569
GO ID Go Term p-value q-value Cluster
GO:0006730 one-carbon compound metabolism 0.000336935 0.918485 Thaps_bicluster_0238
GO:0006096 glycolysis 0.00992032 1 Thaps_bicluster_0238
GO:0008610 lipid biosynthesis 0.0123557 1 Thaps_bicluster_0238
GO:0006094 gluconeogenesis 0.0366334 1 Thaps_bicluster_0238
GO:0006006 glucose metabolism 0.0406241 1 Thaps_bicluster_0238
GO:0015992 proton transport 0.0603434 1 Thaps_bicluster_0238
GO:0006118 electron transport 0.0939001 1 Thaps_bicluster_0238
GO:0006979 response to oxidative stress 0.0948716 1 Thaps_bicluster_0238
GO:0007264 small GTPase mediated signal transduction 0.131822 1 Thaps_bicluster_0238
GO:0006512 ubiquitin cycle 0.139038 1 Thaps_bicluster_0238
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