Phatr_bicluster_0023 Residual: 0.40
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_0023 0.40 Phaeodactylum tricornutum
Displaying 1 - 46 of 46
PHATRDRAFT_13396 nadph:protochlorophyllide oxidoreductase a (PLN00015)

PHATRDRAFT_12155 - nadph:protochlorophyllide oxidoreductase a (PLN00015)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12155
PHATRDRAFT_16375 sec24-like copii protein (Sec24-like)

PHATRDRAFT_13396 - sec24-like copii protein (Sec24-like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13396
PHATRDRAFT_18194 pyrroline-5-carboxylate reductase (PLN02688)

PHATRDRAFT_16375 - pyrroline-5-carboxylate reductase (PLN02688)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16375
PHATRDRAFT_19954 pre-mrna processing protein (WW)

PHATRDRAFT_18194 - pre-mrna processing protein (WW)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_18194
PHATRDRAFT_21350 group i truncated hemoglobin (globin_like superfamily)

PHATRDRAFT_19954 - group i truncated hemoglobin (globin_like superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_19954
PHATRDRAFT_27361 coenzyme a transferase (CoA_trans)

PHATRDRAFT_21350 - coenzyme a transferase (CoA_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21350
PHATRDRAFT_34205 chaperone clpb (ClpB_D2-small)

PHATRDRAFT_26173 - chaperone clpb (ClpB_D2-small)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_26173
PHATRDRAFT_34611 solute carrier family 2 (facilitated glucose transporter)member 13 (SP)

PHATRDRAFT_27361 - solute carrier family 2 (facilitated glucose transporter)member 13 (SP)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27361
PHATRDRAFT_37257 tocopheroltransfer protein (SEC14)

PHATRDRAFT_33873 - tocopheroltransfer protein (SEC14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33873
PHATRDRAFT_39554 (Complex1_LYR_1)

PHATRDRAFT_34205 - (Complex1_LYR_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34205
PHATRDRAFT_40725

PHATRDRAFT_34611 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34611
PHATRDRAFT_41812 morn motif precursor (MORN superfamily)

PHATRDRAFT_3664 - morn motif precursor (MORN superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_3664
PHATRDRAFT_43087

PHATRDRAFT_37257 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37257
PHATRDRAFT_43325

PHATRDRAFT_39554 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39554
PHATRDRAFT_43401

PHATRDRAFT_40725 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40725
PHATRDRAFT_43413 succinate dehydrogenase flavoprotein alpha subunit (PLN00128)

PHATRDRAFT_41812 - succinate dehydrogenase flavoprotein alpha subunit (PLN00128)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41812
PHATRDRAFT_43466 sp2523 cg18768-isoform c

PHATRDRAFT_43087 - sp2523 cg18768-isoform c

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43087
PHATRDRAFT_43503

PHATRDRAFT_43268 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43268
PHATRDRAFT_43725

PHATRDRAFT_43325 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43325
PHATRDRAFT_44347 tipd_dicdi protein tipd (WD40)

PHATRDRAFT_43401 - tipd_dicdi protein tipd (WD40)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43401
PHATRDRAFT_44532 heat shock transcription factor hsf (HSF_DNA-bind superfamily)

PHATRDRAFT_43413 - heat shock transcription factor hsf (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43413
PHATRDRAFT_44659 cytochrome p450 family protein (CypX)

PHATRDRAFT_43466 - cytochrome p450 family protein (CypX)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43466
PHATRDRAFT_44667

PHATRDRAFT_43503 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43503
PHATRDRAFT_44737

PHATRDRAFT_43725 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43725
PHATRDRAFT_44995 lipoprotein

PHATRDRAFT_44347 - lipoprotein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44347
PHATRDRAFT_45229

PHATRDRAFT_44532 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44532
PHATRDRAFT_45393

PHATRDRAFT_44659 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44659
PHATRDRAFT_45682

PHATRDRAFT_44667 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44667
PHATRDRAFT_45933

PHATRDRAFT_44737 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44737
PHATRDRAFT_46033 cna b domain protein

PHATRDRAFT_44995 - cna b domain protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44995
PHATRDRAFT_46647 clip-associating protein 1-like

PHATRDRAFT_45229 - clip-associating protein 1-like

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45229
PHATRDRAFT_46746 heat shock transcription factor hsf (HSF_DNA-bind)

PHATRDRAFT_45393 - heat shock transcription factor hsf (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45393
PHATRDRAFT_46763 receptor protein kinase-like protein

PHATRDRAFT_45682 - receptor protein kinase-like protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45682
PHATRDRAFT_47209

PHATRDRAFT_45933 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45933
PHATRDRAFT_47282 (DUF1990 superfamily)

PHATRDRAFT_46033 - (DUF1990 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46033
PHATRDRAFT_48046

PHATRDRAFT_46647 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46647
PHATRDRAFT_48048 (O-FucT_like)

PHATRDRAFT_46746 - (O-FucT_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46746
PHATRDRAFT_48558

PHATRDRAFT_46763 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46763
PHATRDRAFT_50039

PHATRDRAFT_47209 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47209
PHATRDRAFT_51528 (Gaa1 superfamily)

PHATRDRAFT_47282 - (Gaa1 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47282
PHATRDRAFT_55126 tkl family protein kinase (PKc)

PHATRDRAFT_48046 - tkl family protein kinase (PKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48046

PHATRDRAFT_48048 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48048

PHATRDRAFT_48558 - heat shock factor rhsf2 (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48558

PHATRDRAFT_50039 - multi-sensor hybrid histidine kinase (PAS_9)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50039

PHATRDRAFT_51528 - coproporphyrinogen iii oxidase (PRK07379)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_51528

PHATRDRAFT_55126 - diphosphate--fructose-6-phosphate 1-phosphotransferase (PFK superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55126
GO ID Go Term p-value q-value Cluster
GO:0001539 ciliary or flagellar motility 0.0169488 1 Phatr_bicluster_0023
GO:0015671 oxygen transport 0.0225371 1 Phatr_bicluster_0023
GO:0006561 proline biosynthesis 0.028095 1 Phatr_bicluster_0023
GO:0006355 regulation of transcription, DNA-dependent 0.0327719 1 Phatr_bicluster_0023
GO:0006888 ER to Golgi transport 0.0445878 1 Phatr_bicluster_0023
GO:0006099 tricarboxylic acid cycle 0.0445878 1 Phatr_bicluster_0023
GO:0008643 carbohydrate transport 0.0872703 1 Phatr_bicluster_0023
GO:0006810 transport 0.0915411 1 Phatr_bicluster_0023
GO:0006886 intracellular protein transport 0.204649 1 Phatr_bicluster_0023
GO:0007165 signal transduction 0.236069 1 Phatr_bicluster_0023
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