Phatr_bicluster_0025 Residual: 0.39
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_0025 0.39 Phaeodactylum tricornutum
Displaying 1 - 51 of 51
PHATRDRAFT_10243 tpa_inf: chloroplast light-harvesting complex protein precursor lhcz1 nuclear (Chloroa_b-bind)

PHATRDRAFT_10243 - tpa_inf: chloroplast light-harvesting complex protein precursor lhcz1 nuclear (Chloroa_b-bind)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10243
PHATRDRAFT_13897 tkl family protein kinase (PKc)

PHATRDRAFT_13897 - tkl family protein kinase (PKc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_13897
PHATRDRAFT_14334 phosphoglycerate bisphosphoglycerate mutase family protein (phoE)

PHATRDRAFT_14334 - phosphoglycerate bisphosphoglycerate mutase family protein (phoE)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_14334
PHATRDRAFT_31942 cyclin e2 isoform 1 (CYCLIN)

PHATRDRAFT_31942 - cyclin e2 isoform 1 (CYCLIN)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_31942
PHATRDRAFT_33120 cog3391: uncharacterized conserved protein

PHATRDRAFT_33120 - cog3391: uncharacterized conserved protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33120
PHATRDRAFT_33150

PHATRDRAFT_33150 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33150
PHATRDRAFT_33493 threonyl-trna synthetase (thrS)

PHATRDRAFT_33493 - threonyl-trna synthetase (thrS)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_33493
PHATRDRAFT_37436 (YafJ)

PHATRDRAFT_37436 - (YafJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37436
PHATRDRAFT_37844

PHATRDRAFT_37844 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37844
PHATRDRAFT_37908 chitin synthase 3 (chs-3) (Glyco_tranf_GTA_type superfamily)

PHATRDRAFT_37908 - chitin synthase 3 (chs-3) (Glyco_tranf_GTA_type superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37908
PHATRDRAFT_39147

PHATRDRAFT_39147 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39147
PHATRDRAFT_39777 (DDE_Tnp_1_7 superfamily)

PHATRDRAFT_39777 - (DDE_Tnp_1_7 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39777
PHATRDRAFT_39796

PHATRDRAFT_39796 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39796
PHATRDRAFT_40822 sh3 domain ysc-like 1 (SYLF)

PHATRDRAFT_40822 - sh3 domain ysc-like 1 (SYLF)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_40822
PHATRDRAFT_41483

PHATRDRAFT_41483 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_41483
PHATRDRAFT_43345

PHATRDRAFT_43345 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_43345
PHATRDRAFT_44134 copper resistance b precursor

PHATRDRAFT_44134 - copper resistance b precursor

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44134
PHATRDRAFT_44146 sld5_klula dna replication complex gins protein sld5 (GINS_A_Sld5)

PHATRDRAFT_44146 - sld5_klula dna replication complex gins protein sld5 (GINS_A_Sld5)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44146
PHATRDRAFT_44213

PHATRDRAFT_44213 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44213
PHATRDRAFT_44307

PHATRDRAFT_44307 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44307
PHATRDRAFT_47390 mgc80777 protein (COG1524)

PHATRDRAFT_47390 - mgc80777 protein (COG1524)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47390
PHATRDRAFT_47536 short-chain dehydrogenase reductase sdr (FabI)

PHATRDRAFT_47536 - short-chain dehydrogenase reductase sdr (FabI)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47536
PHATRDRAFT_47599 (DUF21)

PHATRDRAFT_47599 - (DUF21)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47599
PHATRDRAFT_47721

PHATRDRAFT_47721 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47721
PHATRDRAFT_47736

PHATRDRAFT_47736 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47736
PHATRDRAFT_48077

PHATRDRAFT_48077 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48077
PHATRDRAFT_48203

PHATRDRAFT_48203 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48203
PHATRDRAFT_48246 protein familywith a coiled coil-4 domain (Methyltransf_22)

PHATRDRAFT_48246 - protein familywith a coiled coil-4 domain (Methyltransf_22)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48246
PHATRDRAFT_48352

PHATRDRAFT_48352 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48352
PHATRDRAFT_48380

PHATRDRAFT_48380 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48380
PHATRDRAFT_48389 (GGCT_like)

PHATRDRAFT_48389 - (GGCT_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48389
PHATRDRAFT_48494 peptidase s8 andsedolisin (Peptidases_S8_PCSK9_ProteinaseK_like)

PHATRDRAFT_48494 - peptidase s8 andsedolisin (Peptidases_S8_PCSK9_ProteinaseK_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48494
PHATRDRAFT_48574 essential protein involved in intracellular protein transport

PHATRDRAFT_48574 - essential protein involved in intracellular protein transport

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48574
PHATRDRAFT_48640 wax synthase isoform 2 (MBOAT_2)

PHATRDRAFT_48640 - wax synthase isoform 2 (MBOAT_2)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48640
PHATRDRAFT_48700

PHATRDRAFT_48700 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48700
PHATRDRAFT_48724

PHATRDRAFT_48724 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48724
PHATRDRAFT_48761

PHATRDRAFT_48761 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48761
PHATRDRAFT_48972

PHATRDRAFT_48972 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48972
PHATRDRAFT_49015

PHATRDRAFT_49015 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49015
PHATRDRAFT_49156 serine threonine protein kinase and signal transduction histidine kinasewith gaf sensor (COG3899)

PHATRDRAFT_49156 - serine threonine protein kinase and signal transduction histidine kinasewith gaf sensor (COG3899)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49156
PHATRDRAFT_49170 (HSF_DNA-bind superfamily)

PHATRDRAFT_49170 - (HSF_DNA-bind superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49170
PHATRDRAFT_49562

PHATRDRAFT_49562 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49562
PHATRDRAFT_49842 solute carrier family 34 (sodium phosphate)member 2 (Na_Pi_cotrans)

PHATRDRAFT_49842 - solute carrier family 34 (sodium phosphate)member 2 (Na_Pi_cotrans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49842
PHATRDRAFT_50116

PHATRDRAFT_50116 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50116
PHATRDRAFT_50336 heat shock protein 70 (HMGB-UBF_HMG-box)

PHATRDRAFT_50336 - heat shock protein 70 (HMGB-UBF_HMG-box)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50336
PHATRDRAFT_50473

PHATRDRAFT_50473 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50473
PHATRDRAFT_50485 glucose-6-phosphate phosphate- translocator precursor (TPT superfamily)

PHATRDRAFT_50485 - glucose-6-phosphate phosphate- translocator precursor (TPT superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50485
PHATRDRAFT_50582

PHATRDRAFT_50582 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50582
PHATRDRAFT_50585

PHATRDRAFT_50585 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50585
PHATRDRAFT_54818 (Cyt_b561_FRRS1_like)

PHATRDRAFT_54818 - (Cyt_b561_FRRS1_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54818
PHATRDRAFT_55200 h(+)-transporting atpase (ATPase-IIIA_H)

PHATRDRAFT_55200 - h(+)-transporting atpase (ATPase-IIIA_H)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55200
GO ID Go Term p-value q-value Cluster
GO:0006435 threonyl-tRNA aminoacylation 0.00542673 1 Phatr_bicluster_0025
GO:0006817 phosphate transport 0.0188766 1 Phatr_bicluster_0025
GO:0000074 regulation of cell cycle 0.0886914 1 Phatr_bicluster_0025
GO:0009765 photosynthesis light harvesting 0.101113 1 Phatr_bicluster_0025
GO:0006418 tRNA aminoacylation for protein translation 0.132692 1 Phatr_bicluster_0025
GO:0008152 metabolism 0.187614 1 Phatr_bicluster_0025
GO:0006412 protein biosynthesis 0.360385 1 Phatr_bicluster_0025
GO:0006468 protein amino acid phosphorylation 0.380037 1 Phatr_bicluster_0025
GO:0006355 regulation of transcription, DNA-dependent 0.45797 1 Phatr_bicluster_0025
GO:0006508 proteolysis and peptidolysis 0.465714 1 Phatr_bicluster_0025
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