Thaps_bicluster_0151 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_0151 0.31 Thalassiosira pseudonana
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 25 of 25
" class="views-fluidgrid-wrapper clear-block">
12982 AAA superfamily

12982 - AAA superfamily

GO Terms:

GO:0005524, GO:0000166, GO:0017111, GO:0031177

CD Domains:

Go To Gene Page:

12982
19034 HSP70_NBD

19034 - HSP70_NBD

GO Terms:

GO:0005524

CD Domains:

Go To Gene Page:

19034
20911 RNA14

20911 - RNA14

GO Terms:

GO:0005622, GO:0006396, GO:0005215, GO:0006810, GO:0016020

CD Domains:

Go To Gene Page:

20911
21460 Peptidase_C19 superfamily

21460 - Peptidase_C19 superfamily

GO Terms:

GO:0004197, GO:0004221, GO:0006511

CD Domains:

Go To Gene Page:

21460
24445 hypothetical protein

24445 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24445
25321 hypothetical protein

25321 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25321
2569 Methyltransf_32 superfamily

2569 - Methyltransf_32 superfamily

GO Terms:

GO:0008757, GO:0004289, GO:0006508

CD Domains:

Go To Gene Page:

2569
25795 REX4_like

25795 - REX4_like

GO Terms:

GO:0004527, GO:0005622

CD Domains:

Go To Gene Page:

25795
261747 PRK00142

261747 - PRK00142

GO Terms:

NA

CD Domains:

Go To Gene Page:

261747
262858 (IKI3) IKI3

262858 - (IKI3) IKI3

GO Terms:

NA

CD Domains:

Go To Gene Page:

262858
263363 ANK

263363 - ANK

GO Terms:

NA

CD Domains:

Go To Gene Page:

263363
263786 (ZFP20) zf-TAZ

263786 - (ZFP20) zf-TAZ

GO Terms:

GO:0003712, GO:0005634, GO:0006355

CD Domains:

Go To Gene Page:

263786
3009 hypothetical protein

3009 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3009
31404 XRN1

31404 - XRN1

GO Terms:

GO:0004527, GO:0005634

CD Domains:

Go To Gene Page:

31404
35510 SET

35510 - SET

GO Terms:

NA

CD Domains:

Go To Gene Page:

35510
38136 RRM2_PHIP1

38136 - RRM2_PHIP1

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

38136
38827 DEXDc

38827 - DEXDc

GO Terms:

GO:0003700, GO:0006355

CD Domains:

Go To Gene Page:

38827
595 S1_IF1A

595 - S1_IF1A

GO Terms:

GO:0003743, GO:0006413, GO:0003723

CD Domains:

Go To Gene Page:

595
9061 RNA_pol_B_RPB2 superfamily

9061 - RNA_pol_B_RPB2 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

9061
9576 hypothetical protein

9576 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

9576
GO ID Go Term p-value q-value Cluster
GO:0008152 metabolism 0.546944 1 Thaps_bicluster_0151
GO:0006470 protein amino acid dephosphorylation 0.0473882 1 Thaps_bicluster_0151
GO:0006508 proteolysis and peptidolysis 0.424754 1 Thaps_bicluster_0151
GO:0006355 regulation of transcription, DNA-dependent 0.107561 1 Thaps_bicluster_0151
GO:0006396 RNA processing 0.102965 1 Thaps_bicluster_0151
GO:0006413 translational initiation 0.0438152 1 Thaps_bicluster_0151
GO:0006810 transport 0.294845 1 Thaps_bicluster_0151
GO:0006511 ubiquitin-dependent protein catabolism 0.0910605 1 Thaps_bicluster_0151
Log in to post comments