Phatr_bicluster_0006 Residual: 0.56Phaeodactylum 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.

Summary

Title	Residual	Model version	Organism
Phatr_bicluster_0006	0.56		Phaeodactylum tricornutum

Module Plots

Motifs

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Motif 1

Motif 2

Members

Displaying 1 - 70 of 70

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PHATRDRAFT_14945 v-typec subunit family protein (ATP-synt_C superfamily)

PHATRDRAFT_15692 golgi membrane protein sb140 isoform 1 (YIP1 superfamily)

PHATRDRAFT_16442 ormdl family protein (ORMDL superfamily)

PHATRDRAFT_16571 vacuolar type h+-atpase proteolipid subunit (ATP-synt_C superfamily)

PHATRDRAFT_16719 phosphoglucomutase 2 (PGM2)

PHATRDRAFT_16854 hcf101 (high-chlorophyll-fluorescence 101) atp binding (MRP-like)

PHATRDRAFT_19329 potential glutaredoxin (GRX_GRXh_1_2_like)

PHATRDRAFT_21207 (PLN02820)

PHATRDRAFT_22398 abc1 family protein (AarF)

PHATRDRAFT_22677 lactation elevated 1 (AAA superfamily)

PHATRDRAFT_2966 degenerative spermatocyte homolog 1 (PLN02579)

PHATRDRAFT_34419 aminotransferase class v (PLN02651)

PHATRDRAFT_34555

PHATRDRAFT_37393

PHATRDRAFT_38754 loc496288 protein

PHATRDRAFT_38803

PHATRDRAFT_38948 (DUF92 superfamily)

PHATRDRAFT_39217

PHATRDRAFT_40043

PHATRDRAFT_40174 subfamilymember 5 (DnaJ)

PHATRDRAFT_40535

PHATRDRAFT_40830 (LRR_RI superfamily)

PHATRDRAFT_40841

PHATRDRAFT_40942

PHATRDRAFT_40956 gtp-binding nuclear protein ran (PTZ00132)

PHATRDRAFT_40988 cgi-122 protein (GINS_A_psf2)

PHATRDRAFT_41125 chaperonin containingsubunit 8isoform 5 (TCP1_theta)

PHATRDRAFT_41541 enoyl-hydratase isomerase (PRK07509)

PHATRDRAFT_41766

PHATRDRAFT_42461

PHATRDRAFT_42828 glutathione s-transferase domain protein (ECM4)

PHATRDRAFT_43814

PHATRDRAFT_44152 rna recognition(or rnp) domain containing protein (RRM_SF superfamily)

PHATRDRAFT_44195

PHATRDRAFT_44420

PHATRDRAFT_44665

PHATRDRAFT_45778

PHATRDRAFT_4593 major facilitator family transporter (MFS_1)

PHATRDRAFT_46447 alpha beta hydrolase fold (Abhydrolase_6)

PHATRDRAFT_47042 hcf101 (high-chlorophyll-fluorescence 101) atp binding (MRP-like)

PHATRDRAFT_47432 kda class i heat shock protein (ACD_sHsps-like)

PHATRDRAFT_47783

PHATRDRAFT_48041 riboflavin-specific deaminase-like protein (RibD)

PHATRDRAFT_48151

PHATRDRAFT_48183

PHATRDRAFT_48208 metacaspase (Peptidase_C14)

PHATRDRAFT_48280

PHATRDRAFT_48314

PHATRDRAFT_48660 (PDZ superfamily)

PHATRDRAFT_48827

PHATRDRAFT_48855 (Cyt_b561_FRRS1_like)

PHATRDRAFT_49117

PHATRDRAFT_49564 nucleolar protein 9 (COG1341)

PHATRDRAFT_49750 ankyrin unc44 (ANK)

PHATRDRAFT_49763

PHATRDRAFT_49857

PHATRDRAFT_49932 helicase domain protein (HA)

PHATRDRAFT_50047 (CIA30 superfamily)

PHATRDRAFT_50216 protein phosphataseregulatory subunit 1

PHATRDRAFT_50343

PHATRDRAFT_5043 serine incorporatorisoform cra_a (Serinc superfamily)

PHATRDRAFT_50562 astacin-like protein (PLN00052)

PHATRDRAFT_50572 ubiquitin-activating enzyme e1 1 (E1_enzyme_family superfamily)

PHATRDRAFT_5104

PHATRDRAFT_54940

PHATRDRAFT_5537 er lumen protein retaining receptor (ER_lumen_recept)

PHATRDRAFT_5629 membrane protein (Cyt_b561_FRRS1_like)

PHATRDRAFT_8772 principal rna polymerase sigma factor (Sigma70_r2)

GO Enrichment

GO ID	Go Term	p-value	q-value	Cluster
GO:0015031	protein transport	0.0189497	1	Phatr_bicluster_0006
GO:0015986	ATP synthesis coupled proton transport	0.0264586	1	Phatr_bicluster_0006
GO:0009073	aromatic amino acid family biosynthesis	0.0341181	1	Phatr_bicluster_0006
GO:0045454	cell redox homeostasis	0.0408058	1	Phatr_bicluster_0006
GO:0009231	riboflavin biosynthesis	0.0408058	1	Phatr_bicluster_0006
GO:0044267	cellular protein metabolism	0.0671124	1	Phatr_bicluster_0006
GO:0006636	fatty acid desaturation	0.0671124	1	Phatr_bicluster_0006
GO:0006352	transcription initiation	0.0800035	1	Phatr_bicluster_0006
GO:0006725	aromatic compound metabolism	0.129871	1	Phatr_bicluster_0006
GO:0007264	small GTPase mediated signal transduction	0.135918	1	Phatr_bicluster_0006

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_14544

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_14945

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_15692

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_16442

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_16571

Phatr_bicluster_0006 Residual: 0.56Phaeodactylum tricornutum

Module Page Help

What is a module?

Expression Profiles

Motif Locations

Regulators

Motifs

Summary

Module Plots

Motifs

Members

PHATRDRAFT_14544 - v-typec subunit family protein (ATP-synt_C superfamily)

PHATRDRAFT_14945 - golgi membrane protein sb140 isoform 1 (YIP1 superfamily)

PHATRDRAFT_15692 - ormdl family protein (ORMDL superfamily)

PHATRDRAFT_16442 - vacuolar type h+-atpase proteolipid subunit (ATP-synt_C superfamily)

PHATRDRAFT_16571 - phosphoglucomutase 2 (PGM2)

PHATRDRAFT_16719 - hcf101 (high-chlorophyll-fluorescence 101) atp binding (MRP-like)

PHATRDRAFT_16854 - potential glutaredoxin (GRX_GRXh_1_2_like)

PHATRDRAFT_19329 - (PLN02820)

PHATRDRAFT_21207 - abc1 family protein (AarF)

PHATRDRAFT_22398 - lactation elevated 1 (AAA superfamily)

PHATRDRAFT_22677 - degenerative spermatocyte homolog 1 (PLN02579)

PHATRDRAFT_2966 - aminotransferase class v (PLN02651)

PHATRDRAFT_34419 -

PHATRDRAFT_34555 -

PHATRDRAFT_37393 - loc496288 protein

PHATRDRAFT_37452 -

PHATRDRAFT_38754 - (DUF92 superfamily)

PHATRDRAFT_38803 -

PHATRDRAFT_38948 -

PHATRDRAFT_39217 - subfamilymember 5 (DnaJ)

PHATRDRAFT_40043 -

PHATRDRAFT_40174 - (LRR_RI superfamily)

PHATRDRAFT_40535 -

PHATRDRAFT_40830 -

PHATRDRAFT_40841 - gtp-binding nuclear protein ran (PTZ00132)

PHATRDRAFT_40942 - cgi-122 protein (GINS_A_psf2)

PHATRDRAFT_40956 - chaperonin containingsubunit 8isoform 5 (TCP1_theta)

PHATRDRAFT_40988 - enoyl-hydratase isomerase (PRK07509)

PHATRDRAFT_41125 -

PHATRDRAFT_41541 -

PHATRDRAFT_41766 - glutathione s-transferase domain protein (ECM4)

PHATRDRAFT_42461 -

PHATRDRAFT_42828 - rna recognition(or rnp) domain containing protein (RRM_SF superfamily)

PHATRDRAFT_43814 -

PHATRDRAFT_44152 -

PHATRDRAFT_44195 -

PHATRDRAFT_44420 -

PHATRDRAFT_44665 - major facilitator family transporter (MFS_1)

PHATRDRAFT_45778 - alpha beta hydrolase fold (Abhydrolase_6)

PHATRDRAFT_4593 - hcf101 (high-chlorophyll-fluorescence 101) atp binding (MRP-like)

PHATRDRAFT_46447 - kda class i heat shock protein (ACD_sHsps-like)

PHATRDRAFT_47042 -

PHATRDRAFT_47432 - riboflavin-specific deaminase-like protein (RibD)

PHATRDRAFT_47783 -

PHATRDRAFT_48041 -

PHATRDRAFT_48151 - metacaspase (Peptidase_C14)

PHATRDRAFT_48183 -

PHATRDRAFT_48208 -

PHATRDRAFT_48280 - (PDZ superfamily)

PHATRDRAFT_48314 -

PHATRDRAFT_48660 - (Cyt_b561_FRRS1_like)

PHATRDRAFT_48827 -

PHATRDRAFT_48855 - nucleolar protein 9 (COG1341)

PHATRDRAFT_49117 - ankyrin unc44 (ANK)

PHATRDRAFT_49564 -

PHATRDRAFT_49750 -

PHATRDRAFT_49763 - helicase domain protein (HA)

PHATRDRAFT_49857 - (CIA30 superfamily)

PHATRDRAFT_49932 - protein phosphataseregulatory subunit 1

PHATRDRAFT_50047 -

PHATRDRAFT_50216 - serine incorporatorisoform cra_a (Serinc superfamily)

PHATRDRAFT_50343 - astacin-like protein (PLN00052)

PHATRDRAFT_5043 - ubiquitin-activating enzyme e1 1 (E1_enzyme_family superfamily)

PHATRDRAFT_50562 -

PHATRDRAFT_50572 -

PHATRDRAFT_5104 - er lumen protein retaining receptor (ER_lumen_recept)

PHATRDRAFT_54940 - membrane protein (Cyt_b561_FRRS1_like)

PHATRDRAFT_5537 - principal rna polymerase sigma factor (Sigma70_r2)

PHATRDRAFT_5629 - phosphoglycerate mutase (HP_PGM_like)

Phatr_bicluster_0006 Residual: 0.56
Phaeodactylum tricornutum