Thaps_bicluster_0098 Residual: 0.36
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_0098 0.36 Thalassiosira pseudonana
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Displaying 1 - 31 of 31
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14140 PDI_a_family

14140 - PDI_a_family

GO Terms:

GO:0005489, GO:0006118, GO:0003756

CD Domains:

Go To Gene Page:

14140
1747 hypothetical protein

1747 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

1747
1845 (RPN9) PCI

1845 - (RPN9) PCI

GO Terms:

GO:0003677, GO:0003700, GO:0006352, GO:0006355, GO:0016987

CD Domains:

Go To Gene Page:

1845
2160 p23_hB-ind1_like

2160 - p23_hB-ind1_like

GO Terms:

NA

CD Domains:

Go To Gene Page:

2160
21911 PH-like superfamily

21911 - PH-like superfamily

GO Terms:

GO:0007155, GO:0016021

CD Domains:

Go To Gene Page:

21911
22443 hypothetical protein

22443 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

22443
24318 (PSB_3) proteasome_beta_type_4

24318 - (PSB_3) proteasome_beta_type_4

GO Terms:

GO:0004175, GO:0005839, GO:0006511, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

24318
24495 (Tp_CCHH26) regulator [Rayko]

24495 - (Tp_CCHH26) regulator [Rayko]

GO Terms:

GO:0003676, GO:0005634, GO:0008270

CD Domains:

Go To Gene Page:

24495
24560 PDI_a_family

24560 - PDI_a_family

GO Terms:

GO:0005489, GO:0006118, GO:0003756

CD Domains:

Go To Gene Page:

24560
26239 (RPN1) RPN1

26239 - (RPN1) RPN1

GO Terms:

GO:0000074, GO:0016512

CD Domains:

Go To Gene Page:

26239
262525 (PSB5) proteasome_beta_type_5

262525 - (PSB5) proteasome_beta_type_5

GO Terms:

GO:0004175, GO:0005839, GO:0006511, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

262525
26706 (PSA7) proteasome_alpha_type_7

26706 - (PSA7) proteasome_alpha_type_7

GO Terms:

GO:0004175, GO:0005839, GO:0006511, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

26706
26868 (PSA3) proteasome_alpha_type_3

26868 - (PSA3) proteasome_alpha_type_3

GO Terms:

GO:0004175, GO:0005839, GO:0006511, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

26868
269593 (RPT4) RPT1

269593 - (RPT4) RPT1

GO Terms:

GO:0000166, GO:0017111, GO:0005524, GO:0005634, GO:0005737, GO:0016787, GO:0030163, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

269593
28028 RPN6

28028 - RPN6

GO Terms:

GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

28028
32037 (RPT6) RPT1

32037 - (RPT6) RPT1

GO Terms:

GO:0005524, GO:0006139, GO:0019201, GO:0000166, GO:0017111, GO:0005634, GO:0005737, GO:0016787, GO:0030163, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

32037
33649 (PSB6) proteasome_beta_type_6

33649 - (PSB6) proteasome_beta_type_6

GO Terms:

GO:0004175, GO:0005839, GO:0006511, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

33649
33725 (RPN11) MPN_RPN11_CSN5

33725 - (RPN11) MPN_RPN11_CSN5

GO Terms:

GO:0008233, GO:0008234

CD Domains:

Go To Gene Page:

33725
34018 RPN7

34018 - RPN7

GO Terms:

GO:0006118, GO:0016020, GO:0016491, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

34018
34219 hypothetical protein

34219 - hypothetical protein

GO Terms:

GO:0005515

CD Domains:

Go To Gene Page:

34219
37367 FKBP_C

37367 - FKBP_C

GO Terms:

GO:0006457, GO:0003755, GO:0004600, GO:0030051, GO:0042027

CD Domains:

Go To Gene Page:

37367
37861 (RPN3) Rpn3_C

37861 - (RPN3) Rpn3_C

GO Terms:

NA

CD Domains:

Go To Gene Page:

37861
38129 (RPN5) PCI superfamily

38129 - (RPN5) PCI superfamily

GO Terms:

GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

38129
39157 (RPT2) PTZ00361

39157 - (RPT2) PTZ00361

GO Terms:

GO:0000166, GO:0017111, GO:0005524, GO:0005634, GO:0005737, GO:0016787, GO:0030163, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

39157
39802 Peptidase_C19 superfamily

39802 - Peptidase_C19 superfamily

GO Terms:

GO:0005975, GO:0004197, GO:0004221, GO:0006511

CD Domains:

Go To Gene Page:

39802
40483 (PSA4) Ntn_hydrolase superfamily

40483 - (PSA4) Ntn_hydrolase superfamily

GO Terms:

GO:0004175, GO:0005839, GO:0006511, GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

40483
40962 (RPN8) PLN03246

40962 - (RPN8) PLN03246

GO Terms:

GO:0004298, GO:0004299

CD Domains:

Go To Gene Page:

40962
4318 TIM21 superfamily

4318 - TIM21 superfamily

GO Terms:

NA

CD Domains:

Go To Gene Page:

4318
5452 hypothetical protein

5452 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

5452
8292 hypothetical protein

8292 - hypothetical protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

8292
GO ID Go Term p-value q-value Cluster
GO:0006511 ubiquitin-dependent protein catabolism 0.000000000661 0.00000183 Thaps_bicluster_0098
GO:0030163 protein catabolism 0.0000168 0.0464273 Thaps_bicluster_0098
GO:0006352 transcription initiation 0.0525024 1 Thaps_bicluster_0098
GO:0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolism 0.0603434 1 Thaps_bicluster_0098
GO:0006118 electron transport 0.0939001 1 Thaps_bicluster_0098
GO:0007155 cell adhesion 0.117217 1 Thaps_bicluster_0098
GO:0000074 regulation of cell cycle 0.221303 1 Thaps_bicluster_0098
GO:0005975 carbohydrate metabolism 0.268867 1 Thaps_bicluster_0098
GO:0006457 protein folding 0.420718 1 Thaps_bicluster_0098
GO:0006355 regulation of transcription, DNA-dependent 0.731291 1 Thaps_bicluster_0098
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