Phatr_bicluster_0043 Residual: 0.34
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_0043 0.34 Phaeodactylum tricornutum
Displaying 1 - 32 of 32
PHATRDRAFT_11022 peptidyl-prolyl cis-transchloroplast precursor (40 kda thylakoid lumen rotamase) (cyclophilin_TLP40_like)

PHATRDRAFT_11022 - peptidyl-prolyl cis-transchloroplast precursor (40 kda thylakoid lumen rotamase) (cyclophilin_TLP40_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11022
PHATRDRAFT_11373 nadph dehydrogenase (PTZ00318)

PHATRDRAFT_11373 - nadph dehydrogenase (PTZ00318)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11373
PHATRDRAFT_12662

PHATRDRAFT_12662 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_12662
PHATRDRAFT_13537 fe-s-cluster redox enzyme (DRE_TIM_metallolyase superfamily)

PHATRDRAFT_13537 - fe-s-cluster redox enzyme (DRE_TIM_metallolyase superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13537
PHATRDRAFT_15820 tpa_inf: chloroplast light-harvesting complex protein precursor lhcz1 (Chloroa_b-bind)

PHATRDRAFT_15820 - tpa_inf: chloroplast light-harvesting complex protein precursor lhcz1 (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_15820
PHATRDRAFT_20308 ubiquitin-conjugating enzyme 2 (UBCc)

PHATRDRAFT_20308 - ubiquitin-conjugating enzyme 2 (UBCc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_20308
PHATRDRAFT_22418 catalase (KatE)

PHATRDRAFT_22418 - catalase (KatE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_22418
PHATRDRAFT_232 at3g19170 mvi11_8 (COG1026)

PHATRDRAFT_232 - at3g19170 mvi11_8 (COG1026)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_232
PHATRDRAFT_32260

PHATRDRAFT_32260 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32260
PHATRDRAFT_32311

PHATRDRAFT_32311 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32311
PHATRDRAFT_33194

PHATRDRAFT_33194 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33194
PHATRDRAFT_34732 protein tyrosine phosphatase (Y_phosphatase3)

PHATRDRAFT_34732 - protein tyrosine phosphatase (Y_phosphatase3)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_34732
PHATRDRAFT_37272 sjchgc02538 protein (HMG-box)

PHATRDRAFT_37272 - sjchgc02538 protein (HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37272
PHATRDRAFT_38015 dnaj protein homolog atj3 (PTZ00037)

PHATRDRAFT_38015 - dnaj protein homolog atj3 (PTZ00037)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_38015
PHATRDRAFT_42477 soul3-like protein (DUF2358 superfamily)

PHATRDRAFT_42477 - soul3-like protein (DUF2358 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42477
PHATRDRAFT_43157 aquaporin 8 (MIP superfamily)

PHATRDRAFT_43157 - aquaporin 8 (MIP superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43157
PHATRDRAFT_43171 vic family transporter: calcium-activated outward-rectifying potassium ion channel (Ion_trans_2)

PHATRDRAFT_43171 - vic family transporter: calcium-activated outward-rectifying potassium ion channel (Ion_trans_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43171
PHATRDRAFT_43245 (SrmB)

PHATRDRAFT_43245 - (SrmB)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43245
PHATRDRAFT_43266

PHATRDRAFT_43266 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43266
PHATRDRAFT_43551 (ClpS superfamily)

PHATRDRAFT_43551 - (ClpS superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43551
PHATRDRAFT_43587 tpr-repeat containing protein (NrfG)

PHATRDRAFT_43587 - tpr-repeat containing protein (NrfG)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43587
PHATRDRAFT_43729

PHATRDRAFT_43729 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43729
PHATRDRAFT_44374 thioredoxin-like protein (TRX_family)

PHATRDRAFT_44374 - thioredoxin-like protein (TRX_family)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44374
PHATRDRAFT_45510 mgc53673 protein (AFD_class_I superfamily)

PHATRDRAFT_45510 - mgc53673 protein (AFD_class_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45510
PHATRDRAFT_45895

PHATRDRAFT_45895 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45895
PHATRDRAFT_45908 possible-terminal domain

PHATRDRAFT_45908 - possible-terminal domain

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45908
PHATRDRAFT_46119

PHATRDRAFT_46119 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46119
PHATRDRAFT_46199

PHATRDRAFT_46199 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46199
PHATRDRAFT_48361 heat shock factor rhsf2 (HSF_DNA-bind)

PHATRDRAFT_48361 - heat shock factor rhsf2 (HSF_DNA-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48361
PHATRDRAFT_54478 malate synthase (malate_synt_A)

PHATRDRAFT_54478 - malate synthase (malate_synt_A)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54478
PHATRDRAFT_8096 presequence translocase-associated protein import motor subunit (DnaJ)

PHATRDRAFT_8096 - presequence translocase-associated protein import motor subunit (DnaJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_8096
PHATRDRAFT_9896 (AFD_class_I superfamily)

PHATRDRAFT_9896 - (AFD_class_I superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9896
GO ID Go Term p-value q-value Cluster
GO:0006457 protein folding 0.0139775 1 Phatr_bicluster_0043
GO:0006118 electron transport 0.0777423 1 Phatr_bicluster_0043
GO:0006813 potassium ion transport 0.0854465 1 Phatr_bicluster_0043
GO:0006979 response to oxidative stress 0.101687 1 Phatr_bicluster_0043
GO:0006512 ubiquitin cycle 0.156409 1 Phatr_bicluster_0043
GO:0009765 photosynthesis light harvesting 0.160195 1 Phatr_bicluster_0043
GO:0006396 RNA processing 0.222148 1 Phatr_bicluster_0043
GO:0006464 protein modification 0.246382 1 Phatr_bicluster_0043
GO:0006355 regulation of transcription, DNA-dependent 0.254081 1 Phatr_bicluster_0043
GO:0008152 metabolism 0.379876 1 Phatr_bicluster_0043
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