Thaps_bicluster_0026 Residual: 0.39Thalassiosira 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.

Summary

Title	Residual	Model version	Organism
Thaps_bicluster_0026	0.39		Thalassiosira pseudonana

10256 hypothetical protein

10331 hypothetical protein

10404 MscS

10712 hypothetical protein

10714 hypothetical protein

10718 hypothetical protein

10762 hypothetical protein

10806 (Tp_HSF_2.4b) HSF_DNA-bind superfamily

11004 hypothetical protein

11162 Methyltransf_21 superfamily

11795 (Tp_CCCH23) regulator [Rayko]

11963 GH18_chitinase-like superfamily

11981 hypothetical protein

12185 hypothetical protein

12758 PLN00113

16912 IMPase

1915 hypothetical protein

2055 hypothetical protein

21589 GluZincin superfamily

21796 hypothetical protein

21898 hypothetical protein

22121 hypothetical protein

23801 (Tp_HSF_4c) HSF_DNA-bind superfamily

25026 hypothetical protein

25193 hypothetical protein

25613 PI3Kc_like superfamily

261804

261967 (Tp_Hox7) regulator [Rayko]

262000 hypothetical protein

262683

263324

264184 PLN00049

264690 (lipB_1) BPL_LplA_LipB superfamily

268447 hypothetical protein

268546 (PPC1) PEPcase superfamily

268564 Peptidase_C1 superfamily

268987 Glyco_hydro_10 superfamily

27850 (PGAM2) HP_PGM_like

2990 hypothetical protein

3047 EEP superfamily

32211 G10

3238 ANK

3459 Snf7 superfamily

35711 GH16_laminarinase_like

38987 ATM1

3975 hypothetical protein

4048 hypothetical protein

4199 ApbA

4223 DDE_Tnp_1_7 superfamily

4907 hypothetical protein

5377 hypothetical protein

5809 hypothetical protein

6211 hypothetical protein

6684 Tryp_SPc

728 (ELO3) ELO

7513 hypothetical protein

771 DUF647 superfamily

7844 hypothetical protein

8149 AarF

8234 hypothetical protein

8450 DnaJ

8614 hypothetical protein

869 hypothetical protein

918 (Tp_HSF_2.5b) regulator [Rayko]

GO Enrichment

GO ID	Go Term	p-value	q-value	Cluster
GO:0006935	chemotaxis	0.00620219	1	Thaps_bicluster_0026
GO:0001539	ciliary or flagellar motility	0.0245865	1	Thaps_bicluster_0026
GO:0009107	lipoate biosynthesis	0.0245865	1	Thaps_bicluster_0026
GO:0018346	protein amino acid prenylation	0.0306412	1	Thaps_bicluster_0026
GO:0000074	regulation of cell cycle	0.0527164	1	Thaps_bicluster_0026
GO:0006099	tricarboxylic acid cycle	0.0603738	1	Thaps_bicluster_0026
GO:0005975	carbohydrate metabolism	0.0780933	1	Thaps_bicluster_0026
GO:0008654	phospholipid biosynthesis	0.0835234	1	Thaps_bicluster_0026
GO:0008152	metabolism	0.102461	1	Thaps_bicluster_0026
GO:0009401	phosphoenolpyruvate-dependent sugar phosphotransferase system	0.106121	1	Thaps_bicluster_0026

GO Terms:	NA
CD Domains:
Go To Gene Page:	10256

GO Terms:	GO:0001539, GO:0003774, GO:0006935, GO:0016020, GO:0005509, GO:0004339
CD Domains:
Go To Gene Page:	10331

GO Terms:	GO:0016020
CD Domains:
Go To Gene Page:	10404

GO Terms:	NA
CD Domains:
Go To Gene Page:	10712

GO Terms:	NA
CD Domains:
Go To Gene Page:	10714

GO Terms:	GO:0004420, GO:0009058
CD Domains:
Go To Gene Page:	10718

GO Terms:	GO:0003700, GO:0005634, GO:0006355, GO:0003677
CD Domains:
Go To Gene Page:	10806

GO Terms:	GO:0008152, GO:0016787, GO:0005576, GO:0006030, GO:0008061, GO:0004308
CD Domains:
Go To Gene Page:	11963

GO Terms:	GO:0004437, GO:0008934
CD Domains:
Go To Gene Page:	16912

GO Terms:	GO:0008152, GO:0008810
CD Domains:
Go To Gene Page:	21589

GO Terms:	GO:0000287, GO:0008152, GO:0016462
CD Domains:
Go To Gene Page:	22121

GO Terms:	GO:0016773, GO:0008318, GO:0018346, GO:0005351, GO:0009401, GO:0004672, GO:0004682, GO:0004691, GO:0005952, GO:0005956, GO:0008603, GO:0008605
CD Domains:
Go To Gene Page:	25613

GO Terms:	GO:0003677, GO:0003700, GO:0005634, GO:0006355
CD Domains:
Go To Gene Page:	261967

GO Terms:	GO:0005515, GO:0006508, GO:0008236, GO:0019132
CD Domains:
Go To Gene Page:	264184

GO Terms:	GO:0009107, GO:0003824, GO:0006464, GO:0000074, GO:0005634
CD Domains:
Go To Gene Page:	264690

GO Terms:	GO:0005489, GO:0006118
CD Domains:
Go To Gene Page:	268447

GO Terms:	GO:0006099, GO:0008964
CD Domains:
Go To Gene Page:	268546

GO Terms:	GO:0004197, GO:0006508, GO:0008234
CD Domains:
Go To Gene Page:	268564

GO Terms:	GO:0004553, GO:0005975, GO:0003677, GO:0006306, GO:0008170
CD Domains:
Go To Gene Page:	268987

GO Terms:	GO:0003824, GO:0008152, GO:0006096, GO:0016868, GO:0004619, GO:0046537, GO:0046538
CD Domains:
Go To Gene Page:	27850

GO Terms:	GO:0005554, GO:0005634
CD Domains:
Go To Gene Page:	32211

GO Terms:	GO:0005554, GO:0004252, GO:0004289, GO:0008132, GO:0008243, GO:0008991, GO:0016808
CD Domains:
Go To Gene Page:	3459

GO Terms:	GO:0004553, GO:0005975
CD Domains:
Go To Gene Page:	35711

GO Terms:	GO:0005524, GO:0006810, GO:0016021, GO:0042626, GO:0016887, GO:0000166, GO:0017111
CD Domains:
Go To Gene Page:	38987

GO Terms:	GO:0000074, GO:0005634
CD Domains:
Go To Gene Page:	6211

Thaps_bicluster_0026 Residual: 0.39Thalassiosira pseudonana

Module Page Help

What is a module?

Expression Profiles

Motif Locations

Regulators

Motifs

Summary

Module Plots

Motifs

Members

10256 - hypothetical protein

10331 - hypothetical protein

10404 - MscS

10712 - hypothetical protein

10714 - hypothetical protein

10718 - hypothetical protein

10762 - hypothetical protein

10806 - (Tp_HSF_2.4b) HSF_DNA-bind superfamily

11004 - hypothetical protein

11162 - Methyltransf_21 superfamily

11795 - (Tp_CCCH23) regulator [Rayko]

11963 - GH18_chitinase-like superfamily

11981 - hypothetical protein

12185 - hypothetical protein

12758 - PLN00113

16912 - IMPase

1915 - hypothetical protein

2055 - hypothetical protein

21589 - GluZincin superfamily

21796 - hypothetical protein

21898 - hypothetical protein

22121 - hypothetical protein

23801 - (Tp_HSF_4c) HSF_DNA-bind superfamily

25026 - hypothetical protein

25193 - hypothetical protein

25613 - PI3Kc_like superfamily

261804 -

261967 - (Tp_Hox7) regulator [Rayko]

262000 - hypothetical protein

262683 -

263324 -

264184 - PLN00049

264690 - (lipB_1) BPL_LplA_LipB superfamily

268447 - hypothetical protein

268546 - (PPC1) PEPcase superfamily

268564 - Peptidase_C1 superfamily

268987 - Glyco_hydro_10 superfamily

27850 - (PGAM2) HP_PGM_like

2990 - hypothetical protein

3047 - EEP superfamily

32211 - G10

3238 - ANK

3459 - Snf7 superfamily

35711 - GH16_laminarinase_like

38987 - ATM1

3975 - hypothetical protein

4048 - hypothetical protein

4199 - ApbA

4223 - DDE_Tnp_1_7 superfamily

4907 - hypothetical protein

5377 - hypothetical protein

5809 - hypothetical protein

6211 - hypothetical protein

6684 - Tryp_SPc

728 - (ELO3) ELO

7513 - hypothetical protein

771 - DUF647 superfamily

7844 - hypothetical protein

8149 - AarF

8234 - hypothetical protein

8450 - DnaJ

8614 - hypothetical protein

869 - hypothetical protein

918 - (Tp_HSF_2.5b) regulator [Rayko]

GO Enrichment

Comments

Thaps_bicluster_0026 Residual: 0.39
Thalassiosira pseudonana

GO Terms:	GO:0004295, GO:0006508, GO:0004263, GO:0004252, GO:0004289, GO:0008132, GO:0008243, GO:0008991, GO:0016808
CD Domains:
Go To Gene Page:	6684

GO Terms:	GO:0008152, GO:0016491
CD Domains:
Go To Gene Page:	8234

GO Terms:	GO:0006457, GO:0031072, GO:0051082
CD Domains:
Go To Gene Page:	8450