Thaps_bicluster_0274 Residual: 0.39
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_0274 0.39 Thalassiosira pseudonana
Displaying 1 - 23 of 23
10058 hypothetical protein

10058 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10058
11575 hypothetical protein

11575 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11575
1283 (MTS2_1) TGT superfamily

1283 - (MTS2_1) TGT superfamily

GO Terms:

GO:0006400, GO:0008479, GO:0008616

CD Domains:

Go To Gene Page:

1283
1553 PKc_like superfamily

1553 - PKc_like superfamily

GO Terms:

GO:0004672, GO:0005524, GO:0006468, GO:0004713, GO:0004674, GO:0005952, GO:0008603

CD Domains:

Go To Gene Page:

1553
20405 GRX_GRXh_1_2_like

20405 - GRX_GRXh_1_2_like

GO Terms:

GO:0005489, GO:0006118, GO:0045454

CD Domains:

Go To Gene Page:

20405
20804 hypothetical protein

20804 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20804
21069 Mito_carr

21069 - Mito_carr

GO Terms:

GO:0005488, GO:0006810, GO:0016020, GO:0005215, GO:0005743

CD Domains:

Go To Gene Page:

21069
25248 MATE_like superfamily

25248 - MATE_like superfamily

GO Terms:

GO:0000280, GO:0016021

CD Domains:

Go To Gene Page:

25248
262960 TM_PBP1_branched-chain-AA_like superfamily

262960 - TM_PBP1_branched-chain-AA_like superfamily

GO Terms:

GO:0006814, GO:0006885, GO:0015385, GO:0016021, GO:0015299

CD Domains:

Go To Gene Page:

262960
263873 Mito_carr

263873 - Mito_carr

GO Terms:

GO:0005488, GO:0006810, GO:0016020

CD Domains:

Go To Gene Page:

263873
267929 Skp1

267929 - Skp1

GO Terms:

NA

CD Domains:

Go To Gene Page:

267929
3038 hypothetical protein

3038 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3038
31362 (SCS1) PLN00124

31362 - (SCS1) PLN00124

GO Terms:

GO:0003824, GO:0008152, GO:0004775, GO:0009361, GO:0042709

CD Domains:

Go To Gene Page:

31362
31510 TIGR00049

31510 - TIGR00049

GO Terms:

GO:0005554

CD Domains:

Go To Gene Page:

31510
32022 SPFH_paraslipin

32022 - SPFH_paraslipin

GO Terms:

GO:0016020

CD Domains:

Go To Gene Page:

32022
35518 (GYK) PLN02295

35518 - (GYK) PLN02295

GO Terms:

GO:0005975, GO:0004370

CD Domains:

Go To Gene Page:

35518
3560 hypothetical protein

3560 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3560
37585 MECDP_synthase

37585 - MECDP_synthase

GO Terms:

GO:0008685, GO:0016114

CD Domains:

Go To Gene Page:

37585
37920 cyclophilin_ABH_like

37920 - cyclophilin_ABH_like

GO Terms:

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

CD Domains:

Go To Gene Page:

37920
7704 CoA_CoA_reduc

7704 - CoA_CoA_reduc

GO Terms:

GO:0006118, GO:0016491, GO:0015036, GO:0005737, GO:0004362

CD Domains:

Go To Gene Page:

7704
8062 hypothetical protein

8062 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8062
9581 hypothetical protein

9581 - hypothetical protein

GO Terms:

GO:0005529, GO:0005489, GO:0005506, GO:0006118

CD Domains:

Go To Gene Page:

9581
9803 hypothetical protein

9803 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9803
GO ID Go Term p-value q-value Cluster
GO:0000280 nuclear division 0.00330783 1 Thaps_bicluster_0274
GO:0006885 regulation of pH 0.00989276 1 Thaps_bicluster_0274
GO:0016114 terpenoid biosynthesis 0.0131699 1 Thaps_bicluster_0274
GO:0008616 queuosine biosynthesis 0.0131699 1 Thaps_bicluster_0274
GO:0006400 tRNA modification 0.0131699 1 Thaps_bicluster_0274
GO:0045454 cell redox homeostasis 0.0294036 1 Thaps_bicluster_0274
GO:0006814 sodium ion transport 0.0358268 1 Thaps_bicluster_0274
GO:0006118 electron transport 0.0541069 1 Thaps_bicluster_0274
GO:0006810 transport 0.121913 1 Thaps_bicluster_0274
GO:0005975 carbohydrate metabolism 0.221528 1 Thaps_bicluster_0274
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