Organism : Methanococcus maripaludis S2 | Module List :
MMP0637

ArsR family transcriptional regulator

CircVis
Functional Annotations (6)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0637
(Mouseover regulator name to see its description)

MMP0637 is regulated by 10 influences and regulates 10 modules.
Regulators for MMP0637 (10)
Regulator Module Operator
MMP0907
MMP1646
24 combiner
MMP1065 24 tf
MMP1499
MMP1646
24 combiner
MMP1704 24 tf
MMP0168
MMP0907
107 combiner
MMP0386
H2
107 combiner
MMP0460
MMP1100
107 combiner
MMP1100
MMP1442
107 combiner
MMP1376 107 tf
MMP1467
MMP1646
107 combiner

Warning: MMP0637 Does not regulate any modules!

Motif information (de novo identified motifs for modules)

There are 4 motifs predicted.

Motif Table (4)
Motif Id e-value Consensus Motif Logo
709 4.70e-04 taCCaCCa
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710 4.30e+03 GCGAGGG
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871 1.00e-01 tctAtGGtgg
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872 2.40e+02 CCCtccCaGAGCcC
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Motif Help

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.

Motifs of interest can be broadcasted to RegPredict (currently only available for Desulfovibrio vulgaris Hildenborough) in order to compare conservation in similar species. This integrated motif prediction and comparative analysis provides an additional checkpoint for regulatory motif prediction confidence.

Motif e-value: cMonkey tries to identify two motifs per modules in the upstream sequences of the module member genes. Motif e-value is an indicative of the motif co-occurences between the members of the module.Smaller e-values are indicative of significant sequence motifs. Our experience showed that e-values smaller than 10 are generally indicative of significant motifs.

Functional Enrichment for MMP0637

MMP0637 is enriched for 6 functions in 3 categories.
Enrichment Table (6)
Function System
Predicted transcriptional regulators cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
intracellular go/ cellular_component
regulation of transcription, DNA-dependent go/ biological_process
specific transcriptional repressor activity go/ molecular_function
negative regulation of transcription, DNA-dependent go/ biological_process
Module neighborhood information for MMP0637

MMP0637 has total of 58 gene neighbors in modules 24, 107
Gene neighbors (58)
Gene Common Name Description Module membership
MMP0014 truD tRNA pseudouridine synthase D 66, 107
MMP0015 hypothetical protein MMP0015 66, 107
MMP0076 deoxyribonuclease 24, 35
MMP0098 ferredoxin 40, 107
MMP0104 polyferredoxin 95, 107
MMP0105 hypothetical protein MMP0105 4, 107
MMP0106 hypothetical protein MMP0106 107, 140
MMP0134 hypothetical protein MMP0134 24, 92
MMP0212 glycyl-tRNA synthetase 81, 107
MMP0319 cbiL precorrin-2 C-20 methyltransferase 24, 140, 141, 149
MMP0340 pycB pyruvate carboxylase subunit B 24, 86, 120, 141, 149
MMP0419 sodium:neurotransmitter symporter 24, 38
MMP0637 ArsR family transcriptional regulator 24, 107
MMP0655 hypothetical protein MMP0655 24, 38, 52
MMP0679 Na+/H+ antiporter-like protein 24, 38
MMP0702 hypothetical protein MMP0702 24, 38, 162
MMP0713 iorA2 indolepyruvate oxidoreductase subunit alpha 2 24, 47, 86
MMP0714 iorB2 indolepyruvate oxidoreductase subunit beta 24, 47, 86
MMP0715 coenzyme F390 synthetase II 24, 86
MMP0814 hypothetical protein MMP0814 24, 86
MMP0815 hypothetical protein MMP0815 24, 86
MMP0873 hypothetical protein MMP0873 95, 107
MMP0880 aksF isopropylmalate/isohomocitrate dehydrogenase 24, 60, 140, 143
MMP0917 dapF diaminopimelate epimerase 107, 136
MMP0935 hypothetical protein MMP0935 107, 126
MMP0936 aroE shikimate 5-dehydrogenase 66, 107
MMP0953 cbiH precorrin-3B C17-methyltransferase 24, 25, 149
MMP1017 lysC aspartate kinase 24, 60, 112
MMP1038 atpH A1A0 ATPase subunit H 107, 135
MMP1039 atpI V-type ATP synthase subunit I 107, 135
MMP1040 atpK V-type ATP synthase subunit K 107, 135
MMP1041 atpE A1A0 ATPase subunit IE 107, 135
MMP1042 atpC V-type ATP synthase subunit C 107, 135
MMP1043 atpF V-type ATP synthase subunit F 107, 135
MMP1044 atpA V-type ATP synthase subunit A 107, 135
MMP1045 atpB V-type ATP synthase subunit B 107, 135
MMP1046 atpD V-type ATP synthase subunit D 107, 135
MMP1047 hypothetical protein MMP1047 107, 135
MMP1190 FKBP-type peptidylprolyl isomerase 35, 107
MMP1219 putative dinG ATP-dependent helicase 95, 107
MMP1270 bifunctional hexulose-6-phosphate synthase/ribonuclease regulator 24, 38
MMP1337 hydrogenase maturation protease 95, 107
MMP1363 rpoA1 DNA-directed RNA polymerase subunit A' 24, 103, 130
MMP1429 rpm DNA-directed RNA polymerase subunit M 95, 107
MMP1464 ehaQ hypothetical protein MMP1464 107, 133
MMP1465 ehaR hypothetical protein MMP1465 107, 133
MMP1466 ehaS putative CBS domain-containing signal transduction protein 95, 107, 133
MMP1537 cytochrome c heme-binding site 24, 29
MMP1538 transporter component 24, 29
MMP1540 hypothetical protein MMP1540 24, 140
MMP1541 hypothetical protein MMP1541 24, 38
MMP1590 ExsB family protein 24, 51
MMP1659 pyrB aspartate carbamoyltransferase catalytic subunit 24, 111, 122
Unanno_2 None 24, 86
Unanno_3 None 107, 126
Unanno_4 None 24, 86
Unanno_5 None 95, 107
Unanno_60 None 95, 107
Gene Page Help

Network Tab

If the gene is associated with a module(s), its connection to given modules along with other members of that module are shown as network by using CytoscapeWeb. In this view, each green colored circular nodes represent module member genes, purple colored diamonds represent module motifs and red triangles represent regulators. Each node is connected to module (Bicluster) via edges. This representation provides quick overview of all genes, regulators and motifs for modules. It also allows one to see shared genes/motifs/regulators among diferent modules.

Network representation is interactive. You can zoom in/out and move nodes/edges around. Clicking on a node will open up a window to give more details. For genes, Locus tag, organism, genomic coordinates, NCBI gene ID, whether it is transcription factor or not and any associated functional information will be shown. For regulators, number of modules are shown in addition to gene details. For motifs, e-value, consensus sequence and sequence logo will be shown. For modules, expression profile plot, motif information, functional associations and motif locations for each member of the module will be shown.
You can pin information boxes by using button in the box title and open up additional ones on the same screen for comparative analysis.

Regulation Tab

Regulation tab for each gene includes regulatory influences such as environmental factors or transcription factors or their combinations identified by regulatory network inference algorithms.

If the gene is a member of a module, regulators influencing that module are also considered to regulate the gene. Regulators table list total number of regulatory influences, regulators, modules and type of the influence.

You can see description of the regulator inside the tooltip when you mouseover. In certain cases the regulatory influence is predicted to be the result of the combination of two influences. These are indicated as combiner in the column labeled "Operator".

For transcription factors, an additional table next to regulator table will be show. This table show modules that are influenced by the transcription factor.

Motifs Tab

Network inference algorithm uses de novo motif prediction for assigning genes to modules. If there are any motifs identified in the upstream region of a gene, the motif will be shown here. For each motif sequence logo, consensus and e-value will be shown.

Functions Tab

Identification of functional enrichment for the module members is important in associating predicted motifs and regulatory influences with pathways. As described above, the network inference pipeline includes a functional enrichment module by which hypergeometric p-values are used to identify over representation of functional ontology terms among module members.

Network Portal presents functional ontologies from KEGG, GO, TIGRFAM, and COG as separate tables that include function name, type, corrected and uncorrected hypergeometric p-values, and the number of genes assigned to this category out of total number of genes in the module.

Module Members Tab

Identity of gene members in a module may help to identify potential interactions between different functional modules. Therefore, neighbor genes that share the same module(s) with gene under consideration are shown here. For each memebr, gene name, description and modules that contain it are listed.

Help Tab

This help page. More general help can be accessed by clicking help menu in the main navigation bar.

Social Tab

Network Portal is designed to promote collaboration through social interactions. Therefore interested researchers can share information, questions and updates for a particular gene.

Users can use their Disqus, Facebook, Twitter or Google accounts to connect to this page (We recommend Google). Each module and gene page includes comments tab that lists history of the interactions for that gene. You can browse the history, make updates, raise questions and share these activities with social web.

In the next releases of the network portal, we are planning to create personal space for each user where you can share you space that contains all the analysis steps you did along with relevant information.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend
Comments for MMP0637
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Gene Help

Overview

Gene landing pages present genomic, functional, and regulatory information for individual genes. A circular visualization displays connections between the selected gene and genes in the same modules, with as edges drawn between the respective coordinates of the whole genome.

The gene page also lists functional ontology assignments, module membership, and motifs associated with these modules. Genes in the network inherit regulatory influences from the modules to which they belong. Therefore, the regulatory information for each gene is a collection of all regulatory influences on these modules. These are listed as a table that includes influence name, type, and target module. If the gene is a transcription factor, its target modules are also displayed in a table that provides residual values and number of genes.

CircVis

Our circular module explorer is adapted from visquick originally developed by Dick Kreisberg of Ilya Shmulevich lab at ISB for The Cancer Genome Atlas. We use simplified version of visquick to display distribution of module members and their interactions across the genome. This view provides summary of regulation information for a gene. The main components are;
  • 1. All genomic elements for the organism are represented as a circle and each element is separated by black tick marks. In this example chromosome and pDV represent main chromosome and plasmid for D. vulgaris Hildenborough, respectively.
  • 2. Source gene
  • 3. Target genes (other module members)
  • 4. Interactions between source and target genes for a particular module
  • 5. Module(s) that source gene and target genes belong to
  • 6. Visualisation legend