Thaps_bicluster_0048 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_0048 0.39 Thalassiosira pseudonana
" class="views-fluidgrid-wrapper clear-block">
Displaying 1 - 32 of 32
" class="views-fluidgrid-wrapper clear-block">
1015 hypothetical protein

1015 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1015
11320 (DPHA1) PLN02291

11320 - (DPHA1) PLN02291

GO Terms:

GO:0003849, GO:0009073

CD Domains:

Go To Gene Page:

11320
11586 hypothetical protein

11586 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

11586
11756 SURF1 superfamily

11756 - SURF1 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

11756
12052 hypothetical protein

12052 - hypothetical protein

GO Terms:

GO:0003824

CD Domains:

Go To Gene Page:

12052
20959 (Tp_Myb1R4) regulator [Rayko]

20959 - (Tp_Myb1R4) regulator [Rayko]

GO Terms:

GO:0003677, GO:0005634, GO:0006306, GO:0008170

CD Domains:

Go To Gene Page:

20959
22645 hypothetical protein

22645 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22645
22940 ARGLU

22940 - ARGLU

GO Terms:

GO:0004672, GO:0004682, GO:0004691, GO:0005952, GO:0005956, GO:0008603, GO:0008605

CD Domains:

Go To Gene Page:

22940
23473 Cupin_8 superfamily

23473 - Cupin_8 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

23473
24311 hypothetical protein

24311 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

24311
2515 nst superfamily

2515 - nst superfamily

GO Terms:

GO:0005338, GO:0015780, GO:0016021, GO:0000139, GO:0005351, GO:0008643

CD Domains:

Go To Gene Page:

2515
25775 RING

25775 - RING

GO Terms:

GO:0000151, GO:0004842, GO:0008270, GO:0016567

CD Domains:

Go To Gene Page:

25775
260841 CysJ

260841 - CysJ

GO Terms:

GO:0005489, GO:0006118, GO:0016491, GO:0010181, GO:0003958

CD Domains:

Go To Gene Page:

260841
261045 PI3Kc_like superfamily

261045 - PI3Kc_like superfamily

GO Terms:

GO:0016773

CD Domains:

Go To Gene Page:

261045
261132 (PDT1) PLN02517 superfamily

261132 - (PDT1) PLN02517 superfamily

GO Terms:

GO:0004607, GO:0006629, GO:0046027

CD Domains:

Go To Gene Page:

261132
261966 Ndh

261966 - Ndh

GO Terms:

GO:0016491, GO:0051341

CD Domains:

Go To Gene Page:

261966
264016 ATPase-IIB_Ca

264016 - ATPase-IIB_Ca

GO Terms:

GO:0005524, GO:0006812, GO:0015662, GO:0016020, GO:0003824, GO:0008152, GO:0005388, GO:0005509, GO:0006816, GO:0015085, GO:0016820

CD Domains:

Go To Gene Page:

264016
264674 2OG-FeII_Oxy_3 superfamily

264674 - 2OG-FeII_Oxy_3 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

264674
269113 M3_like

269113 - M3_like

GO Terms:

GO:0004222, GO:0006508

CD Domains:

Go To Gene Page:

269113
269735 hypothetical protein

269735 - hypothetical protein

GO Terms:

GO:0003677

CD Domains:

Go To Gene Page:

269735
30400 COG0390

30400 - COG0390

GO Terms:

NA

CD Domains:

Go To Gene Page:

30400
38095 UPF0014 superfamily

38095 - UPF0014 superfamily

GO Terms:

GO:0005524, GO:0016887, GO:0000166, GO:0017111

CD Domains:

Go To Gene Page:

38095
3811 hypothetical protein

3811 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

3811
41521 Peptidase_S10

41521 - Peptidase_S10

GO Terms:

GO:0003824, GO:0004185, GO:0006508, GO:0004187

CD Domains:

Go To Gene Page:

41521
42320 PTZ00464 superfamily

42320 - PTZ00464 superfamily

GO Terms:

GO:0005554

CD Domains:

Go To Gene Page:

42320
5319 DPPIV_N

5319 - DPPIV_N

GO Terms:

GO:0003824, GO:0006508, GO:0008236, GO:0004274, GO:0016020

CD Domains:

Go To Gene Page:

5319
6597 hypothetical protein

6597 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6597
6605 hypothetical protein

6605 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6605
7840 hypothetical protein

7840 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

7840
8051 PLN02517 superfamily

8051 - PLN02517 superfamily

GO Terms:

GO:0004607, GO:0006629, GO:0005524, GO:0016887, GO:0004622

CD Domains:

Go To Gene Page:

8051
9174 DUF563

9174 - DUF563

GO Terms:

NA

CD Domains:

Go To Gene Page:

9174
9908 PRK14902

9908 - PRK14902

GO Terms:

NA

CD Domains:

Go To Gene Page:

9908
GO ID Go Term p-value q-value Cluster
GO:0006629 lipid metabolism 0.00347268 1 Thaps_bicluster_0048
GO:0015780 nucleotide-sugar transport 0.0154159 1 Thaps_bicluster_0048
GO:0006816 calcium ion transport 0.0184724 1 Thaps_bicluster_0048
GO:0009073 aromatic amino acid family biosynthesis 0.02152 1 Thaps_bicluster_0048
GO:0008643 carbohydrate transport 0.0426071 1 Thaps_bicluster_0048
GO:0006508 proteolysis and peptidolysis 0.0557851 1 Thaps_bicluster_0048
GO:0051341 regulation of oxidoreductase activity 0.0690961 1 Thaps_bicluster_0048
GO:0006306 DNA methylation 0.0863737 1 Thaps_bicluster_0048
GO:0006812 cation transport 0.125531 1 Thaps_bicluster_0048
GO:0016567 protein ubiquitination 0.219149 1 Thaps_bicluster_0048
Log in to post comments