Phatr_bicluster_0002 Residual: 0.43Phaeodactylum 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_0002	0.43		Phaeodactylum tricornutum

Module Plots

Motifs

" class="views-fluidgrid-wrapper clear-block">

Motif 1

Motif 2

Members

Displaying 1 - 78 of 78

" class="views-fluidgrid-wrapper clear-block">

PHATRDRAFT_13856 solute carrier family 25 (carnitine acylcarnitine translocase)member 20 (Mito_carr)

PHATRDRAFT_14607 pms2 postmeiotic segregation incre (mutl)

PHATRDRAFT_14735 qs (quinolinate synthase) quinolinate synthetase a (NadA superfamily)

PHATRDRAFT_15160 dynactin 25 kda subunit (LbetaH superfamily)

PHATRDRAFT_16991 uric acid-xanthine permease (Sulfate_transp superfamily)

PHATRDRAFT_21791 novel protein (ArfGap)

PHATRDRAFT_22554 alg2 protein (Glycosyltransferase_GTB_type superfamily)

PHATRDRAFT_22568 glycolate oxidase (FMN_dh)

PHATRDRAFT_23723 at3g05290 t12h1_26 (Mito_carr)

PHATRDRAFT_2394 cysteinyl-trna synthetase family protein (nt_trans superfamily)

PHATRDRAFT_2739 leucine-rich repeat transmembrane protein

PHATRDRAFT_2936 ubiquitin carboxyl-terminal hydrolase family protein (UCH)

PHATRDRAFT_30638 gpi-anchor transamidase precursor (Peptidase_C13 superfamily)

PHATRDRAFT_33251 conserved hypothetical

PHATRDRAFT_33624 matrix metalloproteinase (Peptidase_M11 superfamily)

PHATRDRAFT_37038 taurine catabolism dioxygenase (CAS_like superfamily)

PHATRDRAFT_37404 copia protein (gag-int-pol protein)

PHATRDRAFT_37459 probable hydrolase (HAD superfamily)

PHATRDRAFT_37827

PHATRDRAFT_38403

PHATRDRAFT_38429

PHATRDRAFT_38848 xpg i-region familyexpressed (PIN_SF superfamily)

PHATRDRAFT_38978

PHATRDRAFT_39081 pas pac sensor hybrid histidine kinase (HATPase_c)

PHATRDRAFT_39546

PHATRDRAFT_39576

PHATRDRAFT_39610

PHATRDRAFT_39727 at4g32140 f10n7_50 (RhaT)

PHATRDRAFT_39996

PHATRDRAFT_40023 core 1 udp-galactose:n-acetylgalactosamine-alpha-r beta- galactosy

PHATRDRAFT_40381

PHATRDRAFT_40474

PHATRDRAFT_40550

PHATRDRAFT_40610

PHATRDRAFT_40722

PHATRDRAFT_40760

PHATRDRAFT_41489

PHATRDRAFT_41584

PHATRDRAFT_41620

PHATRDRAFT_42585 zinc finger in n-recognin family protein (zf-UBR)

PHATRDRAFT_43830 (Vps35 superfamily)

PHATRDRAFT_44021 potassium channel (Ion_trans_2)

PHATRDRAFT_44169

PHATRDRAFT_44206

PHATRDRAFT_46971 xpg-like endonuclease cg10670-pa (PIN_SF superfamily)

PHATRDRAFT_47252

PHATRDRAFT_47583 short-chain dehydrogenase reductase sdr (SDR_c)

PHATRDRAFT_47796

PHATRDRAFT_47798 flavin-containing monooxygenase

PHATRDRAFT_47833

PHATRDRAFT_48021

PHATRDRAFT_48289 dna helicase (DEXDc)

PHATRDRAFT_48335

PHATRDRAFT_48393 2-oxoglutarate dehydrogenase e3 component (dihydrolipoamide dehydrogenase) (Lpd)

PHATRDRAFT_48422

PHATRDRAFT_48525 zinc finger (zf-DHHC)

PHATRDRAFT_48581

PHATRDRAFT_48605

PHATRDRAFT_48645 pyridoxamine 5-phosphate oxidase-fmn-binding (Pyridox_oxidase)

PHATRDRAFT_48667 heat shock factor 6 (HSF_DNA-bind superfamily)

PHATRDRAFT_48752 (SfsA superfamily)

PHATRDRAFT_49072

PHATRDRAFT_49198 (Sec7_N superfamily)

PHATRDRAFT_49612

PHATRDRAFT_49902 asparagine synthase (glutamine-hydrolyzing) or related prot (Asn_Synthase_B_C)

PHATRDRAFT_49934 hyperpolarization-cyclic nucleotide-gated potassium channel 3

PHATRDRAFT_50003

PHATRDRAFT_50093

PHATRDRAFT_50142

PHATRDRAFT_50274 dna polymerase epsilon subunit 2 isoform 1 (DNA_pol_E_B)

PHATRDRAFT_50359

PHATRDRAFT_50401 glutamyl-trnaamidotransferase subunit a (GGCT_like superfamily)

PHATRDRAFT_51283 splicing factorsubunit 4 (RRM2_SF3B4)

PHATRDRAFT_52547 protein kinase (S_TKc)

PHATRDRAFT_54879

PHATRDRAFT_7181

PHATRDRAFT_7959 myb-like dna-binding domain containing protein (SANT)

PHATRDRAFT_8524 loc494751 protein

GO Enrichment

GO ID	Go Term	p-value	q-value	Cluster
GO:0051336	regulation of hydrolase activity	0.000631938	1	Phatr_bicluster_0002
GO:0006423	cysteinyl-tRNA aminoacylation	0.0198767	1	Phatr_bicluster_0002
GO:0006281	DNA repair	0.0210699	1	Phatr_bicluster_0002
GO:0006529	asparagine biosynthesis	0.0264173	1	Phatr_bicluster_0002
GO:0006289	nucleotide-excision repair	0.0329159	1	Phatr_bicluster_0002
GO:0006298	mismatch repair	0.0393727	1	Phatr_bicluster_0002
GO:0043087	regulation of GTPase activity	0.0710389	1	Phatr_bicluster_0002
GO:0006813	potassium ion transport	0.125523	1	Phatr_bicluster_0002
GO:0006810	transport	0.132184	1	Phatr_bicluster_0002
GO:0006260	DNA replication	0.160121	1	Phatr_bicluster_0002

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_13856

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_14607

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_14735

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_15160

GO Terms:	NA
CD Domains:
Go To Gene Page:	PHATRDRAFT_16991

Phatr_bicluster_0002 Residual: 0.43Phaeodactylum tricornutum

Module Page Help

What is a module?

Expression Profiles

Motif Locations

Regulators

Motifs

Summary

Module Plots

Motifs

Members

PHATRDRAFT_13856 - solute carrier family 25 (carnitine acylcarnitine translocase)member 20 (Mito_carr)

PHATRDRAFT_14607 - pms2 postmeiotic segregation incre (mutl)

PHATRDRAFT_14735 - qs (quinolinate synthase) quinolinate synthetase a (NadA superfamily)

PHATRDRAFT_15160 - dynactin 25 kda subunit (LbetaH superfamily)

PHATRDRAFT_16991 - uric acid-xanthine permease (Sulfate_transp superfamily)

PHATRDRAFT_21791 - novel protein (ArfGap)

PHATRDRAFT_22554 - alg2 protein (Glycosyltransferase_GTB_type superfamily)

PHATRDRAFT_22568 - glycolate oxidase (FMN_dh)

PHATRDRAFT_23723 - at3g05290 t12h1_26 (Mito_carr)

PHATRDRAFT_2394 - cysteinyl-trna synthetase family protein (nt_trans superfamily)

PHATRDRAFT_2739 - leucine-rich repeat transmembrane protein

PHATRDRAFT_2936 - ubiquitin carboxyl-terminal hydrolase family protein (UCH)

PHATRDRAFT_30638 - gpi-anchor transamidase precursor (Peptidase_C13 superfamily)

PHATRDRAFT_33251 - conserved hypothetical

PHATRDRAFT_33624 - matrix metalloproteinase (Peptidase_M11 superfamily)

PHATRDRAFT_37038 - taurine catabolism dioxygenase (CAS_like superfamily)

PHATRDRAFT_37404 - copia protein (gag-int-pol protein)

PHATRDRAFT_37459 - probable hydrolase (HAD superfamily)

PHATRDRAFT_37827 -

PHATRDRAFT_38403 -

PHATRDRAFT_38429 -

PHATRDRAFT_38848 - xpg i-region familyexpressed (PIN_SF superfamily)

PHATRDRAFT_38978 -

PHATRDRAFT_39081 - pas pac sensor hybrid histidine kinase (HATPase_c)

PHATRDRAFT_39546 -

PHATRDRAFT_39576 -

PHATRDRAFT_39610 -

PHATRDRAFT_39727 - at4g32140 f10n7_50 (RhaT)

PHATRDRAFT_39996 -

PHATRDRAFT_40023 - core 1 udp-galactose:n-acetylgalactosamine-alpha-r beta- galactosy

PHATRDRAFT_40381 -

PHATRDRAFT_40474 -

PHATRDRAFT_40550 -

PHATRDRAFT_40610 -

PHATRDRAFT_40722 -

PHATRDRAFT_40760 -

PHATRDRAFT_41489 -

PHATRDRAFT_41584 -

PHATRDRAFT_41620 -

PHATRDRAFT_42585 - zinc finger in n-recognin family protein (zf-UBR)

PHATRDRAFT_43830 - (Vps35 superfamily)

PHATRDRAFT_44021 - potassium channel (Ion_trans_2)

PHATRDRAFT_44169 -

PHATRDRAFT_44206 -

PHATRDRAFT_46971 - xpg-like endonuclease cg10670-pa (PIN_SF superfamily)

PHATRDRAFT_47252 -

PHATRDRAFT_47583 - short-chain dehydrogenase reductase sdr (SDR_c)

PHATRDRAFT_47796 -

PHATRDRAFT_47798 - flavin-containing monooxygenase

PHATRDRAFT_47833 -

PHATRDRAFT_48021 -

PHATRDRAFT_48289 - dna helicase (DEXDc)

PHATRDRAFT_48335 -

PHATRDRAFT_48393 - 2-oxoglutarate dehydrogenase e3 component (dihydrolipoamide dehydrogenase) (Lpd)

PHATRDRAFT_48422 -

PHATRDRAFT_48525 - zinc finger (zf-DHHC)

PHATRDRAFT_48581 -

PHATRDRAFT_48605 -

PHATRDRAFT_48645 - pyridoxamine 5-phosphate oxidase-fmn-binding (Pyridox_oxidase)

PHATRDRAFT_48667 - heat shock factor 6 (HSF_DNA-bind superfamily)

PHATRDRAFT_48752 - (SfsA superfamily)

PHATRDRAFT_49072 -

PHATRDRAFT_49198 - (Sec7_N superfamily)

PHATRDRAFT_49612 -

PHATRDRAFT_49902 - asparagine synthase (glutamine-hydrolyzing) or related prot (Asn_Synthase_B_C)

PHATRDRAFT_49934 - hyperpolarization-cyclic nucleotide-gated potassium channel 3

PHATRDRAFT_50003 -

PHATRDRAFT_50093 -

PHATRDRAFT_50142 -

Phatr_bicluster_0002 Residual: 0.43
Phaeodactylum tricornutum