Phatr_bicluster_0010 Residual: 0.55Phaeodactylum 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_0010	0.55		Phaeodactylum tricornutum

Module Plots

Motifs

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Motif 1

Motif 2

Members

Displaying 1 - 68 of 68

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PHATRDRAFT_15641 transcription factor dp-2 (e2f dimerization partner 2) (DP superfamily)

PHATRDRAFT_16581 novel protein (Methyltransf_28)

PHATRDRAFT_16944 high-mobility group box 2 (HMG-box)

PHATRDRAFT_25739 histidyl-trna synthetase-like (HisS)

PHATRDRAFT_34004 xylitol dehydrogenase (fabG)

PHATRDRAFT_34031

PHATRDRAFT_34433

PHATRDRAFT_34936

PHATRDRAFT_35923

PHATRDRAFT_36118

PHATRDRAFT_37227 (Alginate_lyase)

PHATRDRAFT_37406

PHATRDRAFT_38631 heat shock 105kda 110kda proteinisoform cra_a

PHATRDRAFT_38980 6-phosphogluconolactonase-like protein (SugarP_isomerase superfamily)

PHATRDRAFT_39107

PHATRDRAFT_39218

PHATRDRAFT_39403

PHATRDRAFT_40832 novel proteinvertebrate histidine triad nucleotide binding protein 3(zgc:136256) (DcpS_C)

PHATRDRAFT_40834

PHATRDRAFT_41064

PHATRDRAFT_41365 fibronectin-binding a domain protein (COG1293)

PHATRDRAFT_41393 (DUF924 superfamily)

PHATRDRAFT_41599

PHATRDRAFT_41756 hypothetical repeat protein

PHATRDRAFT_42742 loc100004107 protein (HrpA)

PHATRDRAFT_43363

PHATRDRAFT_43412 heat shock transcription factor hsf4 (HSF_DNA-bind superfamily)

PHATRDRAFT_43692 cna b domain protein

PHATRDRAFT_43797 (GRX_family)

PHATRDRAFT_43821 small heat shock protein (ACD_sHsps-like)

PHATRDRAFT_43850 rad18_schpo postreplication repair e3 ubiquitin-protein ligase rad18 (rad18 homolog) (rad18)

PHATRDRAFT_44208 zinc finger constans-like protein (CCT)

PHATRDRAFT_44281 type b (COesterase)

PHATRDRAFT_44606

PHATRDRAFT_45693 mitochondria associated granulocyte macrophage csf signaling molecule (Pam16 superfamily)

PHATRDRAFT_46052

PHATRDRAFT_46096

PHATRDRAFT_46402

PHATRDRAFT_46968 rna polymerase beta subunit (LUC7)

PHATRDRAFT_47541 (Glyco_trans_1_2)

PHATRDRAFT_47577

PHATRDRAFT_48164

PHATRDRAFT_48192 (Hr-like)

PHATRDRAFT_48383

PHATRDRAFT_48554

PHATRDRAFT_48555 (HMGB-UBF_HMG-box)

PHATRDRAFT_48680

PHATRDRAFT_48891 salivary gland secretion 1 cg3047-pa (MPP_superfamily superfamily)

PHATRDRAFT_48910 prolyl 4-alpha subunit domain protein (P4Hc)

PHATRDRAFT_48915

PHATRDRAFT_49062 extracellular ribonuclease nuclease fusion protein (Endonuclease_1 superfamily)

PHATRDRAFT_49118 tyrosine phosphatase (SEC14 superfamily)

PHATRDRAFT_49238 family protein

PHATRDRAFT_49268 metal dependent phosphohydrolase

PHATRDRAFT_49544 dmt family transporter: drug metabolite (RhaT)

PHATRDRAFT_49557 mgc159930 protein (LPLAT_MGAT-like)

PHATRDRAFT_49613 heat shock protein (HSF_DNA-bind)

PHATRDRAFT_49637

PHATRDRAFT_49724 glycerophosphoryl diester phosphodiesterase (PI-PLCc_GDPD_SF superfamily)

PHATRDRAFT_50183 2fe-2s ferredoxin

PHATRDRAFT_50283 rna polymerase sigma factor (Sig70-cyanoRpoD)

PHATRDRAFT_50353

PHATRDRAFT_50517 2-nitropropane dioxygenase (TIM_phosphate_binding superfamily)

PHATRDRAFT_54926 chitin binding protein

PHATRDRAFT_55004 (Carboxyl_trans)

PHATRDRAFT_55013

PHATRDRAFT_55138 protein n-methyltransferase

GO Enrichment

GO ID	Go Term	p-value	q-value	Cluster
GO:0006310	DNA recombination	0.0000316	0.0730573	Phatr_bicluster_0010
GO:0006355	regulation of transcription, DNA-dependent	0.000638898	1	Phatr_bicluster_0010
GO:0006427	histidyl-tRNA aminoacylation	0.0103473	1	Phatr_bicluster_0010
GO:0006071	glycerol metabolism	0.0205926	1	Phatr_bicluster_0010
GO:0006352	transcription initiation	0.0605726	1	Phatr_bicluster_0010
GO:0000074	regulation of cell cycle	0.16266	1	Phatr_bicluster_0010
GO:0019538	protein metabolism	0.171397	1	Phatr_bicluster_0010
GO:0007242	intracellular signaling cascade	0.197092	1	Phatr_bicluster_0010
GO:0006418	tRNA aminoacylation for protein translation	0.238237	1	Phatr_bicluster_0010
GO:0016567	protein ubiquitination	0.314583	1	Phatr_bicluster_0010

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_14805

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_15641

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_16581

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_16944

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_25739

Phatr_bicluster_0010 Residual: 0.55Phaeodactylum tricornutum

Module Page Help

What is a module?

Expression Profiles

Motif Locations

Regulators

Motifs

Summary

Module Plots

Motifs

Members

PHATRDRAFT_14805 - transcription factor dp-2 (e2f dimerization partner 2) (DP superfamily)

PHATRDRAFT_15641 - novel protein (Methyltransf_28)

PHATRDRAFT_16581 - high-mobility group box 2 (HMG-box)

PHATRDRAFT_16944 - histidyl-trna synthetase-like (HisS)

PHATRDRAFT_25739 - xylitol dehydrogenase (fabG)

PHATRDRAFT_34004 -

PHATRDRAFT_34031 -

PHATRDRAFT_34433 -

PHATRDRAFT_34936 -

PHATRDRAFT_35923 -

PHATRDRAFT_36118 - (Alginate_lyase)

PHATRDRAFT_37227 -

PHATRDRAFT_37406 - heat shock 105kda 110kda proteinisoform cra_a

PHATRDRAFT_38631 - 6-phosphogluconolactonase-like protein (SugarP_isomerase superfamily)

PHATRDRAFT_38980 -

PHATRDRAFT_39107 -

PHATRDRAFT_39218 -

PHATRDRAFT_39403 - novel proteinvertebrate histidine triad nucleotide binding protein 3(zgc:136256) (DcpS_C)

PHATRDRAFT_40832 -

PHATRDRAFT_40834 -

PHATRDRAFT_41064 - fibronectin-binding a domain protein (COG1293)

PHATRDRAFT_41365 - (DUF924 superfamily)

PHATRDRAFT_41393 -

PHATRDRAFT_41599 - hypothetical repeat protein

PHATRDRAFT_41756 - loc100004107 protein (HrpA)

PHATRDRAFT_42742 -

PHATRDRAFT_43363 - heat shock transcription factor hsf4 (HSF_DNA-bind superfamily)

PHATRDRAFT_43412 - cna b domain protein

PHATRDRAFT_43692 - (GRX_family)

PHATRDRAFT_43797 - small heat shock protein (ACD_sHsps-like)

PHATRDRAFT_43821 - rad18_schpo postreplication repair e3 ubiquitin-protein ligase rad18 (rad18 homolog) (rad18)

PHATRDRAFT_43850 - zinc finger constans-like protein (CCT)

PHATRDRAFT_44208 - type b (COesterase)

PHATRDRAFT_44281 -

PHATRDRAFT_44606 - mitochondria associated granulocyte macrophage csf signaling molecule (Pam16 superfamily)

PHATRDRAFT_45693 -

PHATRDRAFT_46052 -

PHATRDRAFT_46096 -

PHATRDRAFT_46402 - rna polymerase beta subunit (LUC7)

PHATRDRAFT_46968 - (Glyco_trans_1_2)

PHATRDRAFT_47541 -

PHATRDRAFT_47577 -

PHATRDRAFT_48164 - (Hr-like)

PHATRDRAFT_48192 -

PHATRDRAFT_48383 -

PHATRDRAFT_48554 - (HMGB-UBF_HMG-box)

PHATRDRAFT_48555 -

PHATRDRAFT_48680 - salivary gland secretion 1 cg3047-pa (MPP_superfamily superfamily)

PHATRDRAFT_48891 - prolyl 4-alpha subunit domain protein (P4Hc)

PHATRDRAFT_48910 -

PHATRDRAFT_48915 - extracellular ribonuclease nuclease fusion protein (Endonuclease_1 superfamily)

PHATRDRAFT_49062 - tyrosine phosphatase (SEC14 superfamily)

PHATRDRAFT_49118 - family protein

PHATRDRAFT_49238 - metal dependent phosphohydrolase

PHATRDRAFT_49268 - dmt family transporter: drug metabolite (RhaT)

PHATRDRAFT_49544 - mgc159930 protein (LPLAT_MGAT-like)

PHATRDRAFT_49557 - heat shock protein (HSF_DNA-bind)

PHATRDRAFT_49613 -

PHATRDRAFT_49637 - glycerophosphoryl diester phosphodiesterase (PI-PLCc_GDPD_SF superfamily)

PHATRDRAFT_49724 - 2fe-2s ferredoxin

PHATRDRAFT_50183 - rna polymerase sigma factor (Sig70-cyanoRpoD)

PHATRDRAFT_50283 -

PHATRDRAFT_50353 - 2-nitropropane dioxygenase (TIM_phosphate_binding superfamily)

PHATRDRAFT_50517 - chitin binding protein

PHATRDRAFT_54926 - (Carboxyl_trans)

PHATRDRAFT_55004 -

PHATRDRAFT_55013 - protein n-methyltransferase

PHATRDRAFT_55138 -

GO Enrichment

Phatr_bicluster_0010 Residual: 0.55
Phaeodactylum tricornutum