Phatr_bicluster_0057 Residual: 0.32
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_0057 0.32 Phaeodactylum tricornutum
Displaying 1 - 39 of 39
PHATRDRAFT_10209 copg2 protein (SEC21)

PHATRDRAFT_10209 - copg2 protein (SEC21)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10209
PHATRDRAFT_10862 h(+)-transporting atpase (V-ATPase_C superfamily)

PHATRDRAFT_10862 - h(+)-transporting atpase (V-ATPase_C superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_10862
PHATRDRAFT_11016 cytochrome c oxidase subunit 6b-1 (Cyt_c_Oxidase_VIb)

PHATRDRAFT_11016 - cytochrome c oxidase subunit 6b-1 (Cyt_c_Oxidase_VIb)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_11016
PHATRDRAFT_16856 (Glyco_hydro_1)

PHATRDRAFT_16856 - (Glyco_hydro_1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_16856
PHATRDRAFT_21664 abc transporter (3a01205)

PHATRDRAFT_21664 - abc transporter (3a01205)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_21664
PHATRDRAFT_24978 h+lysosomal (vacuolar proton pump)beta 56 58isoform 2 (V-ATPase_V1_B)

PHATRDRAFT_24978 - h+lysosomal (vacuolar proton pump)beta 56 58isoform 2 (V-ATPase_V1_B)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_24978
PHATRDRAFT_25752 phg1a protein (EMP70 superfamily)

PHATRDRAFT_25752 - phg1a protein (EMP70 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_25752
PHATRDRAFT_27190 udp-galactose 4-epimerase-like protein (PLN02240)

PHATRDRAFT_27190 - udp-galactose 4-epimerase-like protein (PLN02240)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_27190
PHATRDRAFT_32065 unconventional myosin heavy chain

PHATRDRAFT_32065 - unconventional myosin heavy chain

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_32065
PHATRDRAFT_35568

PHATRDRAFT_35568 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35568
PHATRDRAFT_35766 elongation factor 2 (PLN00116)

PHATRDRAFT_35766 - elongation factor 2 (PLN00116)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_35766
PHATRDRAFT_36311

PHATRDRAFT_36311 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36311
PHATRDRAFT_36390 glutathione s-transferase (Gst)

PHATRDRAFT_36390 - glutathione s-transferase (Gst)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36390
PHATRDRAFT_36403 uncoordinated family member (unc-54)

PHATRDRAFT_36403 - uncoordinated family member (unc-54)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_36403
PHATRDRAFT_37843

PHATRDRAFT_37843 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_37843
PHATRDRAFT_39650

PHATRDRAFT_39650 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39650
PHATRDRAFT_39942 (D-hex-6-P-epi_like)

PHATRDRAFT_39942 - (D-hex-6-P-epi_like)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_39942
PHATRDRAFT_42504 sec14 cytosolic factor (SEC14)

PHATRDRAFT_42504 - sec14 cytosolic factor (SEC14)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42504
PHATRDRAFT_42590 (SET)

PHATRDRAFT_42590 - (SET)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42590
PHATRDRAFT_42755 zip family transporter: zinc ion (Zip superfamily)

PHATRDRAFT_42755 - zip family transporter: zinc ion (Zip superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_42755
PHATRDRAFT_44320

PHATRDRAFT_44320 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44320
PHATRDRAFT_44576

PHATRDRAFT_44576 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44576
PHATRDRAFT_44765 (Condensin2nSMC)

PHATRDRAFT_44765 - (Condensin2nSMC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_44765
PHATRDRAFT_45055

PHATRDRAFT_45055 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45055
PHATRDRAFT_45331 protein c14orf138 homolog (Methyltransf_16 superfamily)

PHATRDRAFT_45331 - protein c14orf138 homolog (Methyltransf_16 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_45331
PHATRDRAFT_46838 nuf2_neucr probable kinetochore protein nuf-2 (Nuf2 superfamily)

PHATRDRAFT_46838 - nuf2_neucr probable kinetochore protein nuf-2 (Nuf2 superfamily)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_46838
PHATRDRAFT_47206 polycystin 2 (Ion_trans)

PHATRDRAFT_47206 - polycystin 2 (Ion_trans)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47206
PHATRDRAFT_47418 viral a-type inclusion (Smc)

PHATRDRAFT_47418 - viral a-type inclusion (Smc)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47418
PHATRDRAFT_47575 peroxidase family protein

PHATRDRAFT_47575 - peroxidase family protein

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47575
PHATRDRAFT_47670 emp nonaspanin domain family protein (EMP70)

PHATRDRAFT_47670 - emp nonaspanin domain family protein (EMP70)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_47670
PHATRDRAFT_48124

PHATRDRAFT_48124 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48124
PHATRDRAFT_48725

PHATRDRAFT_48725 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_48725
PHATRDRAFT_49302

PHATRDRAFT_49302 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_49302
PHATRDRAFT_50065

PHATRDRAFT_50065 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50065
PHATRDRAFT_50344

PHATRDRAFT_50344 -

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_50344
PHATRDRAFT_54296 meiotic nuclear divisions 1 homolog (Mnd1)

PHATRDRAFT_54296 - meiotic nuclear divisions 1 homolog (Mnd1)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_54296
PHATRDRAFT_55069 probable trifunctonal: enoyl-coa hydratase and delta3-cis-delta2-trans-enoyl-coa isomerase and 3-hydroxyacyl-coa dehydrogenase oxidoreductase protein (fadJ)

PHATRDRAFT_55069 - probable trifunctonal: enoyl-coa hydratase and delta3-cis-delta2-trans-enoyl-coa isomerase and 3-hydroxyacyl-coa dehydrogenase oxidoreductase protein (fadJ)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_55069
PHATRDRAFT_9444 solute carrier familymember b2 (UAA)

PHATRDRAFT_9444 - solute carrier familymember b2 (UAA)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9444
PHATRDRAFT_9697 transcription factor btf3 (NAC)

PHATRDRAFT_9697 - transcription factor btf3 (NAC)

GO Terms:

NA

CD Domains:

Go To Gene Page:

PHATRDRAFT_9697
GO ID Go Term p-value q-value Cluster
GO:0006012 galactose metabolism 0.000145417 0.334459 Phatr_bicluster_0057
GO:0009225 nucleotide-sugar metabolism 0.0273554 1 Phatr_bicluster_0057
GO:0006811 ion transport 0.0426705 1 Phatr_bicluster_0057
GO:0030001 metal ion transport 0.0614964 1 Phatr_bicluster_0057
GO:0006812 cation transport 0.101699 1 Phatr_bicluster_0057
GO:0006810 transport 0.172614 1 Phatr_bicluster_0057
GO:0005975 carbohydrate metabolism 0.222271 1 Phatr_bicluster_0057
GO:0016567 protein ubiquitination 0.249948 1 Phatr_bicluster_0057
GO:0006412 protein biosynthesis 0.478179 1 Phatr_bicluster_0057
GO:0006118 electron transport 0.606744 1 Phatr_bicluster_0057
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