Thaps_bicluster_0249 Residual: 0.31
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_0249 0.31 Thalassiosira pseudonana
Displaying 1 - 25 of 25
10899 hypothetical protein

10899 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

10899
13485 ncs2

13485 - ncs2

GO Terms:

GO:0005215, GO:0006810, GO:0016020

CD Domains:

Go To Gene Page:

13485
15093 Peptidase_S10 superfamily

15093 - Peptidase_S10 superfamily

GO Terms:

GO:0003824, GO:0004185, GO:0006508, GO:0004186, GO:0004258

CD Domains:

Go To Gene Page:

15093
16390 Peptidase_C1A

16390 - Peptidase_C1A

GO Terms:

GO:0004197, GO:0006508, GO:0008234, GO:0016946

CD Domains:

Go To Gene Page:

16390
20816 PLPDE_IV superfamily

20816 - PLPDE_IV superfamily

GO Terms:

GO:0003824, GO:0008152, GO:0004084

CD Domains:

Go To Gene Page:

20816
20984 hypothetical protein

20984 - hypothetical protein

GO Terms:

GO:0007242, GO:0004308

CD Domains:

Go To Gene Page:

20984
22395 hypothetical protein

22395 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22395
22864 (SDH) GcvT

22864 - (SDH) GcvT

GO Terms:

GO:0006118, GO:0016491, GO:0004047, GO:0005737, GO:0006546, GO:0008480

CD Domains:

Go To Gene Page:

22864
23047 hypothetical protein

23047 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

23047
23867 hypothetical protein

23867 - hypothetical protein

GO Terms:

GO:0008757, GO:0004719, GO:0006464

CD Domains:

Go To Gene Page:

23867
25895 hypothetical protein

25895 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25895
260934 PLPDE_IV superfamily

260934 - PLPDE_IV superfamily

GO Terms:

GO:0003824, GO:0008152, GO:0004084

CD Domains:

Go To Gene Page:

260934
261124 PLN02819

261124 - PLN02819

GO Terms:

GO:0006118, GO:0016491

CD Domains:

Go To Gene Page:

261124
261158 calcium channel

261158 - calcium channel

GO Terms:

GO:0005509, GO:0005261, GO:0006812, GO:0016020, GO:0005216, GO:0006811

CD Domains:

Go To Gene Page:

261158
262515 CLN3 superfamily

262515 - CLN3 superfamily

GO Terms:

GO:0016020

CD Domains:

Go To Gene Page:

262515
268594 tyr_nico_aTase

268594 - tyr_nico_aTase

GO Terms:

GO:0009058, GO:0016847, GO:0003824, GO:0016769, GO:0006519, GO:0008483, GO:0004838

CD Domains:

Go To Gene Page:

268594
269095 AdoMet_MTases

269095 - AdoMet_MTases

GO Terms:

GO:0008757, GO:0004672, GO:0005524, GO:0006468, GO:0050342

CD Domains:

Go To Gene Page:

269095
269127 (ACD3) ACAD superfamily

269127 - (ACD3) ACAD superfamily

GO Terms:

GO:0003995, GO:0006118, GO:0016491, GO:0016937, GO:0017099, GO:0019109

CD Domains:

Go To Gene Page:

269127
28651 (AAT1_1) PLN02644

28651 - (AAT1_1) PLN02644

GO Terms:

GO:0003985

CD Domains:

Go To Gene Page:

28651
32067 PTZ00182

32067 - PTZ00182

GO Terms:

GO:0004739

CD Domains:

Go To Gene Page:

32067
35094 Aldolase_II superfamily

35094 - Aldolase_II superfamily

GO Terms:

GO:0006564, GO:0016616

CD Domains:

Go To Gene Page:

35094
38360 Peptidase_C1 superfamily

38360 - Peptidase_C1 superfamily

GO Terms:

GO:0006508, GO:0008234

CD Domains:

Go To Gene Page:

38360
3906 Mito_carr

3906 - Mito_carr

GO Terms:

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

CD Domains:

Go To Gene Page:

3906
795 TPP_E1_PDC_ADC_BCADC

795 - TPP_E1_PDC_ADC_BCADC

GO Terms:

GO:0008152, GO:0016624, GO:0003863, GO:0017086

CD Domains:

Go To Gene Page:

795
GO ID Go Term p-value q-value Cluster
GO:0006519 amino acid and derivative metabolism 0.00434153 1 Thaps_bicluster_0249
GO:0006546 glycine catabolism 0.0215288 1 Thaps_bicluster_0249
GO:0006564 L-serine biosynthesis 0.0384333 1 Thaps_bicluster_0249
GO:0006811 ion transport 0.0754573 1 Thaps_bicluster_0249
GO:0008152 metabolism 0.094279 1 Thaps_bicluster_0249
GO:0006118 electron transport 0.1053 1 Thaps_bicluster_0249
GO:0006508 proteolysis and peptidolysis 0.125896 1 Thaps_bicluster_0249
GO:0007242 intracellular signaling cascade 0.167666 1 Thaps_bicluster_0249
GO:0006812 cation transport 0.171312 1 Thaps_bicluster_0249
GO:0006810 transport 0.189129 1 Thaps_bicluster_0249
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