Thaps_bicluster_0229 Residual: 0.40
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_0229 0.40 Thalassiosira pseudonana
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Displaying 1 - 35 of 35
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10129 Dtyr_deacylase superfamily

10129 - Dtyr_deacylase superfamily

GO Terms:

GO:0005737, GO:0016788, GO:0019478, GO:0004518, GO:0042578

CD Domains:

Go To Gene Page:

10129
11342 RNA_pol_Rpc4 superfamily

11342 - RNA_pol_Rpc4 superfamily

GO Terms:

GO:0003677, GO:0003899, GO:0006350, GO:0006399

CD Domains:

Go To Gene Page:

11342
1692 hypothetical protein

1692 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1692
18538 Dynein_heavy superfamily

18538 - Dynein_heavy superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

18538
20962 hypothetical protein

20962 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20962
20972 hypothetical protein

20972 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

20972
21281 hypothetical protein

21281 - hypothetical protein

GO Terms:

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

CD Domains:

Go To Gene Page:

21281
21800 Peptidase_M14_like superfamily

21800 - Peptidase_M14_like superfamily

GO Terms:

GO:0008152, GO:0016788

CD Domains:

Go To Gene Page:

21800
22385 SAC3_GANP

22385 - SAC3_GANP

GO Terms:

NA

CD Domains:

Go To Gene Page:

22385
22623 KH-I

22623 - KH-I

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

22623
22978 Aar2_C

22978 - Aar2_C

GO Terms:

NA

CD Domains:

Go To Gene Page:

22978
23810 (PPS1) PRK06464

23810 - (PPS1) PRK06464

GO Terms:

GO:0016310, GO:0016772, GO:0005524, GO:0016301, GO:0006094, GO:0008986

CD Domains:

Go To Gene Page:

23810
24017 hypothetical protein

24017 - hypothetical protein

GO Terms:

GO:0008152, GO:0006508, GO:0008237, GO:0008270

CD Domains:

Go To Gene Page:

24017
2443 hypothetical protein

2443 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2443
24820 hypothetical protein

24820 - hypothetical protein

GO Terms:

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

CD Domains:

Go To Gene Page:

24820
25725 TatA

25725 - TatA

GO Terms:

GO:0008565, GO:0015031

CD Domains:

Go To Gene Page:

25725
25906 hypothetical protein

25906 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

25906
260906 pyridoxal_pyridoxamine_kinase

260906 - pyridoxal_pyridoxamine_kinase

GO Terms:

GO:0008478

CD Domains:

Go To Gene Page:

260906
261260 PHO4

261260 - PHO4

GO Terms:

GO:0005315, GO:0006817, GO:0016020

CD Domains:

Go To Gene Page:

261260
261802 Aldo_ket_red

261802 - Aldo_ket_red

GO Terms:

GO:0016491, GO:0008708, GO:0008726, GO:0016614, GO:0018446, GO:0018447, GO:0018448, GO:0018449, GO:0018450, GO:0042469, GO:0045703

CD Domains:

Go To Gene Page:

261802
262677

262677 -

GO Terms:

GO:0008757

CD Domains:

Go To Gene Page:

262677
268574 Tim17

268574 - Tim17

GO Terms:

GO:0005743, GO:0008565, GO:0015031

CD Domains:

Go To Gene Page:

268574
268661 (pab1) RRM_SF superfamily

268661 - (pab1) RRM_SF superfamily

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

268661
268872 SET

268872 - SET

GO Terms:

NA

CD Domains:

Go To Gene Page:

268872
269976 SRPBCC superfamily

269976 - SRPBCC superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

269976
2941 hypothetical protein

2941 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

2941
30550 Utp11

30550 - Utp11

GO Terms:

GO:0006364, GO:0030529

CD Domains:

Go To Gene Page:

30550
31783 PrmA

31783 - PrmA

GO Terms:

GO:0008757

CD Domains:

Go To Gene Page:

31783
34730 carb_red_sniffer_like_SDR_c

34730 - carb_red_sniffer_like_SDR_c

GO Terms:

GO:0008152, GO:0016491, GO:0051341

CD Domains:

Go To Gene Page:

34730
35274 RRM_Srp1p_AtRSp31_like

35274 - RRM_Srp1p_AtRSp31_like

GO Terms:

GO:0003676

CD Domains:

Go To Gene Page:

35274
35748 Dynein_heavy superfamily

35748 - Dynein_heavy superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

35748
36958 PKc_like superfamily

36958 - PKc_like superfamily

GO Terms:

GO:0004672, GO:0005524, GO:0006468

CD Domains:

Go To Gene Page:

36958
5497 hypothetical protein

5497 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5497
6648 hypothetical protein

6648 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

6648
GO ID Go Term p-value q-value Cluster
GO:0006399 tRNA metabolism 0.00351458 1 Thaps_bicluster_0229
GO:0019478 D-amino acid catabolism 0.00351458 1 Thaps_bicluster_0229
GO:0015031 protein transport 0.00964735 1 Thaps_bicluster_0229
GO:0006817 phosphate transport 0.017457 1 Thaps_bicluster_0229
GO:0006364 rRNA processing 0.027793 1 Thaps_bicluster_0229
GO:0006094 gluconeogenesis 0.0312156 1 Thaps_bicluster_0229
GO:0016310 phosphorylation 0.0447927 1 Thaps_bicluster_0229
GO:0051341 regulation of oxidoreductase activity 0.0779563 1 Thaps_bicluster_0229
GO:0006350 transcription 0.100523 1 Thaps_bicluster_0229
GO:0008152 metabolism 0.167146 1 Thaps_bicluster_0229
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