Organism : Methanococcus maripaludis S2 | Module List :
MMP0799

TetR family transcriptional regulator Member

CircVis
Functional Annotations (5)
Function System
Transcriptional regulator cog/ cog
sequence-specific DNA binding transcription factor activity go/ molecular_function
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 MMP0799
(Mouseover regulator name to see its description)

MMP0799 is regulated by 6 influences and regulates 1 modules.
Regulators for MMP0799 (6)
Regulator Module Operator
H2 23 ef
MMP0791 23 tf
MMP1100 23 tf
H2 9 ef
MMP0629 9 tf
MMP1100 9 tf

Warning: MMP0799 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
679 2.10e-01 TGaCtGATTAaTCAA
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680 5.20e+00 gGttaTgtgggtagcAc
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707 3.00e-06 ttgGGgGa
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708 3.70e+01 GGccaTgccgttagtcTagGG
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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 MMP0799

MMP0799 is enriched for 5 functions in 3 categories.
Module neighborhood information for MMP0799

MMP0799 has total of 48 gene neighbors in modules 9, 23
Gene neighbors (48)
Gene Common Name Description Module membership
Antisense_22 None 9, 113
MMP0035 hypothetical protein MMP0035 23, 67
MMP0057 cofH FO synthase subunit 2 9, 44
MMP0069 methylated-DNA--protein-cysteine methyltransferase 23, 150
MMP0113 hypothetical protein MMP0113 23, 75, 142
MMP0115 nitroreductase 2, 23, 159
MMP0138 fdhA formate dehydrogenase subunit alpha 9, 44
MMP0139 fdhB formate dehydrogenase subunit beta 9, 101
MMP0172 hypothetical protein MMP0172 9, 43
MMP0321 hypothetical protein MMP0321 23, 90
MMP0322 rfcB replication factor C large subunit 23, 67
MMP0347 hypothetical protein MMP0347 9, 124
MMP0476 hypothetical protein MMP0476 23, 90
MMP0477 hypothetical protein MMP0477 23, 90
MMP0486 hypothetical protein MMP0486 9, 62
MMP0496 glutamate synthase subunit-related 23, 159
MMP0528 hypothetical protein MMP0528 23, 150
MMP0563 hypothetical protein MMP0563 23, 124
MMP0742 hypothetical protein MMP0742 23, 49
MMP0791 TetR family transcriptional regulator Member 9, 90
MMP0792 membrane protein 9, 22
MMP0793 hypothetical protein MMP0793 9, 22
MMP0799 TetR family transcriptional regulator Member 9, 23
MMP0818 frcG coenzyme F420-reducing hydrogenase subunit gamma 9, 131
MMP0819 frcD coenzyme F420-reducing hydrogenase subunit delta 9, 131
MMP0822 vhcG coenzyme F420-non-reducing hydrogenase subunit gamma 9, 114
MMP0824 vhcB coenzyme F420-non-reducing hydrogenase subunit beta 9, 114
MMP0997 blue (type1) copper domain-containing protein 23, 43, 90, 125
MMP1019 PEGA domain-containing protein 23, 150
MMP1053 hdrB2 heterodisulfide reductase subunit B2 9, 65
MMP1054 hdrC2 heterodisulfide reductase subunit C2 9, 65
MMP1224 ABC-type amino acid transport/signal transduction systems periplasmic component-related 23, 90
MMP1297 fdhB formate dehydrogenase subunit beta 9, 113
MMP1298 fdhA formate dehydrogenase subunit alpha 9, 113
MMP1299 carbonic anhydrase 9, 113
MMP1300 hypothetical protein MMP1300 9, 113
MMP1301 fdhC formate/nitrite transporter 9, 113
MMP1302 hypothetical protein MMP1302 9, 113
MMP1329 ferredoxin 23, 159
MMP1378 hypothetical protein MMP1378 9, 114
MMP1553 rdxA nitroreductase family protein 23, 90, 159
MMP1642 ATP/GTP-binding motif-containing protein 9, 123
Unanno_18 None 9, 108
Unanno_39 None 23, 33
Unanno_45 None 9, 38
Unanno_50 None 9, 108
Unanno_52 None 23, 90
Unanno_7 None 23, 46
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 MMP0799
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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