Phatr_bicluster_0137 Residual: 0.31
Phaeodactylum tricornutum

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
Phatr_bicluster_0137 0.31 Phaeodactylum tricornutum
Displaying 1 - 31 of 31
PHATRDRAFT_27972 glutaredoxin 3 (GRX_PICOT_like)

PHATRDRAFT_27972 - glutaredoxin 3 (GRX_PICOT_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27972
PHATRDRAFT_33569

PHATRDRAFT_33569 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33569
PHATRDRAFT_33867 novel protein (2A060601)

PHATRDRAFT_33867 - novel protein (2A060601)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33867
PHATRDRAFT_34233

PHATRDRAFT_34233 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34233
PHATRDRAFT_35030

PHATRDRAFT_35030 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35030
PHATRDRAFT_35224

PHATRDRAFT_35224 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35224
PHATRDRAFT_35419 hsf8_lycesheat shock factor protein hsf8 (heat shock transcription factor 8) (hstf 8) (heat stress transcription factor) (HSF_DNA-bind superfamily)

PHATRDRAFT_35419 - hsf8_lycesheat shock factor protein hsf8 (heat shock transcription factor 8) (hstf 8) (heat stress transcription factor) (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35419
PHATRDRAFT_40228

PHATRDRAFT_40228 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40228
PHATRDRAFT_40453 neurological oncogenic ventral antigen protein (PCBP_like_KH)

PHATRDRAFT_40453 - neurological oncogenic ventral antigen protein (PCBP_like_KH)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40453
PHATRDRAFT_42722 tpr repeat protein (TPR)

PHATRDRAFT_42451 - tpr repeat protein (TPR)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42451
PHATRDRAFT_42861

PHATRDRAFT_42670 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42670
PHATRDRAFT_43298

PHATRDRAFT_42722 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42722
PHATRDRAFT_44426 atp binding protein kinase

PHATRDRAFT_42861 - atp binding protein kinase

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42861
PHATRDRAFT_45099 phosphoglycerate bisphosphoglycerate mutase (HP)

PHATRDRAFT_43298 - phosphoglycerate bisphosphoglycerate mutase (HP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43298
PHATRDRAFT_45149 peptidylprolyl isomerase-like 4 (RRM_PPIL4)

PHATRDRAFT_44426 - peptidylprolyl isomerase-like 4 (RRM_PPIL4)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44426
PHATRDRAFT_45206 tkl family protein kinase (ANK)

PHATRDRAFT_45099 - tkl family protein kinase (ANK)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45099
PHATRDRAFT_45399 pentatricopeptiderepeat-containing protein

PHATRDRAFT_45149 - pentatricopeptiderepeat-containing protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45149
PHATRDRAFT_45558 hsf-type dna-binding domain containing protein (HSF_DNA-bind)

PHATRDRAFT_45206 - hsf-type dna-binding domain containing protein (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45206
PHATRDRAFT_45596

PHATRDRAFT_45399 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45399
PHATRDRAFT_45862 major facilitator superfamily mfs_1 (MFS_1)

PHATRDRAFT_45558 - major facilitator superfamily mfs_1 (MFS_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45558
PHATRDRAFT_46015 receptor protein notch1

PHATRDRAFT_45596 - receptor protein notch1

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45596
PHATRDRAFT_46029

PHATRDRAFT_45862 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45862
PHATRDRAFT_46134 possible ferredoxin (2fe-2s)

PHATRDRAFT_46015 - possible ferredoxin (2fe-2s)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46015
PHATRDRAFT_46164 (FH2)

PHATRDRAFT_46029 - (FH2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46029
PHATRDRAFT_46535 n-terminal acetyltransferase related protein (RimI)

PHATRDRAFT_46134 - n-terminal acetyltransferase related protein (RimI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46134
PHATRDRAFT_54656

PHATRDRAFT_46164 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46164
PHATRDRAFT_8663 myb-like dna-bindingshaqkyf class family protein (SANT)

PHATRDRAFT_46535 - myb-like dna-bindingshaqkyf class family protein (SANT)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46535
PHATRDRAFT_9252 small heat shock protein (ACD_sHsps_p23-like)

PHATRDRAFT_54656 - small heat shock protein (ACD_sHsps_p23-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54656
PHATRDRAFT_9327 cdp-alcohol phosphatidyltransferase (CDP-OH_P_transf superfamily)

PHATRDRAFT_8663 - cdp-alcohol phosphatidyltransferase (CDP-OH_P_transf superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8663

PHATRDRAFT_9252 - membrane protein (Rhomboid)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9252

PHATRDRAFT_9327 - seca_syny3 preprotein translocase subunit seca (secA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9327
GO ID Go Term p-value q-value Cluster
GO:0017038 protein import 0.00321067 1 Phatr_bicluster_0137
GO:0016043 cell organization and biogenesis 0.00641182 1 Phatr_bicluster_0137
GO:0006605 protein targeting 0.0191218 1 Phatr_bicluster_0137
GO:0008654 phospholipid biosynthesis 0.0285555 1 Phatr_bicluster_0137
GO:0006468 protein amino acid phosphorylation 0.102976 1 Phatr_bicluster_0137
GO:0006886 intracellular protein transport 0.121253 1 Phatr_bicluster_0137
GO:0006355 regulation of transcription, DNA-dependent 0.153654 1 Phatr_bicluster_0137
GO:0006457 protein folding 0.317339 1 Phatr_bicluster_0137
GO:0006810 transport 0.466944 1 Phatr_bicluster_0137
GO:0006118 electron transport 0.531402 1 Phatr_bicluster_0137
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