Thaps_bicluster_0066 Residual: 0.42
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_0066 0.42 Thalassiosira pseudonana
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Displaying 1 - 34 of 34
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14389 (HDC) PLN03032

14389 - (HDC) PLN03032

GO Terms:

GO:0006520, GO:0016831, GO:0004782

CD Domains:

Go To Gene Page:

14389
17859 DER1 superfamily

17859 - DER1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

17859
20607 hypothetical protein

20607 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20607
20983 DUF760

20983 - DUF760

GO Terms:

GO:0005509

CD Domains:

Go To Gene Page:

20983
21291 hypothetical protein

21291 - hypothetical protein

GO Terms:

GO:0005509, GO:0004308

CD Domains:

Go To Gene Page:

21291
21519 hypothetical protein

21519 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

21519
21600 Armet superfamily

21600 - Armet superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

21600
2171 hypothetical protein

2171 - hypothetical protein

GO Terms:

GO:0005509

CD Domains:

Go To Gene Page:

2171
22547 hypothetical protein

22547 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22547
2280 hypothetical protein

2280 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2280
25605 (trpAB) Trp-synth_B

25605 - (trpAB) Trp-synth_B

GO Terms:

GO:0003824, GO:0008152, GO:0004834, GO:0006568

CD Domains:

Go To Gene Page:

25605
268061 hypothetical protein

268061 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

268061
30915 prmA

30915 - prmA

GO Terms:

GO:0008757

CD Domains:

Go To Gene Page:

30915
34340 hypothetical protein

34340 - hypothetical protein

GO Terms:

GO:0005489, GO:0006118

CD Domains:

Go To Gene Page:

34340
34771 (MTF1) PLN02285

34771 - (MTF1) PLN02285

GO Terms:

GO:0003910, GO:0005524, GO:0006260, GO:0006281, GO:0006310, GO:0009058, GO:0016742, GO:0004479

CD Domains:

Go To Gene Page:

34771
35780 rplC

35780 - rplC

GO Terms:

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

CD Domains:

Go To Gene Page:

35780
3588 hypothetical protein

3588 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3588
36456 eIF-5_eIF-2B superfamily

36456 - eIF-5_eIF-2B superfamily

GO Terms:

GO:0003743, GO:0006413

CD Domains:

Go To Gene Page:

36456
5514 NADB_Rossmann superfamily

5514 - NADB_Rossmann superfamily

GO Terms:

GO:0008152, GO:0016491, GO:0004090

CD Domains:

Go To Gene Page:

5514
6555 hypothetical protein

6555 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6555
9049 hypothetical protein

9049 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9049
9787 hypothetical protein

9787 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9787
ThpsCp004 (rpl19) ribosomal protein L19

ThpsCp004 - (rpl19) ribosomal protein L19

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp004
ThpsCp024 (rpl35) ribosomal protein L35

ThpsCp024 - (rpl35) ribosomal protein L35

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp024
ThpsCp038 (ycf3) photosystem I assembly protein Ycf3

ThpsCp038 - (ycf3) photosystem I assembly protein Ycf3

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp038
ThpsCp045 (rps14) ribosomal protein S14

ThpsCp045 - (rps14) ribosomal protein S14

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp045
ThpsCp079 (rpl21) ribosomal protein L21

ThpsCp079 - (rpl21) ribosomal protein L21

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp079
ThpsCp080 (rpl27) ribosomal protein L27

ThpsCp080 - (rpl27) ribosomal protein L27

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp080
ThpsCp095 (rpl3) ribosomal protein L3

ThpsCp095 - (rpl3) ribosomal protein L3

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp095
ThpsCp126 (thiG) thiamin biosynthesis protein G

ThpsCp126 - (thiG) thiamin biosynthesis protein G

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp126
ThpsCp135 (secA) preprotein translocase subunit SecA

ThpsCp135 - (secA) preprotein translocase subunit SecA

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp135
ThpsCp136 (rpl27) ribosomal protein L27

ThpsCp136 - (rpl27) ribosomal protein L27

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp136
ThpsCp137 (rpl21) ribosomal protein L21

ThpsCp137 - (rpl21) ribosomal protein L21

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCp137
ThpsCt022 (trnH(gug))

ThpsCt022 - (trnH(gug))

GO Terms:

NA

CD Domains:

Go To Gene Page:

ThpsCt022
GO ID Go Term p-value q-value Cluster
GO:0009058 biosynthesis 0.118319 1 Thaps_bicluster_0066
GO:0008152 metabolism 0.235335 1 Thaps_bicluster_0066
GO:0006412 protein biosynthesis 0.319237 1 Thaps_bicluster_0066
GO:0006118 electron transport 0.463588 1 Thaps_bicluster_0066
GO:0006568 tryptophan metabolism 0.0135745 1 Thaps_bicluster_0066
GO:0006310 DNA recombination 0.0424129 1 Thaps_bicluster_0066
GO:0006520 amino acid metabolism 0.0467809 1 Thaps_bicluster_0066
GO:0006413 translational initiation 0.053299 1 Thaps_bicluster_0066
GO:0006260 DNA replication 0.0768533 1 Thaps_bicluster_0066
GO:0006281 DNA repair 0.0998737 1 Thaps_bicluster_0066
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