Organism : Methanococcus maripaludis S2 | Module List :
MMP0742

hypothetical protein MMP0742

CircVis
Functional Annotations (2)
Function System
Uncharacterized conserved protein cog/ cog
regulation of cell cycle go/ biological_process
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP0742
(Mouseover regulator name to see its description)

MMP0742 is regulated by 6 influences and regulates 1 modules.
Regulators for MMP0742 (6)
Regulator Module Operator
H2 23 ef
MMP0791 23 tf
MMP1100 23 tf
H2 49 ef
MMP0460 49 tf
MMP0499
MMP1065
49 combiner

Warning: MMP0742 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
707 3.00e-06 ttgGGgGa
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708 3.70e+01 GGccaTgccgttagtcTagGG
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759 1.20e+00 tagATatattGgtGa
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760 1.90e+01 caAgTcTGgTGg
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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 MMP0742

MMP0742 is enriched for 2 functions in 3 categories.
Enrichment Table (2)
Function System
Uncharacterized conserved protein cog/ cog
regulation of cell cycle go/ biological_process
Module neighborhood information for MMP0742

MMP0742 has total of 56 gene neighbors in modules 23, 49
Gene neighbors (56)
Gene Common Name Description Module membership
Antisense_13 None 49, 129
Antisense_24 None 5, 49, 90
MMP0020 nickel responsive regulator 49, 123
MMP0035 hypothetical protein MMP0035 23, 67
MMP0036 tfe transcription initiation factor E subunit alpha 49, 87, 92, 129
MMP0063 argB acetylglutamate kinase 49, 151
MMP0069 methylated-DNA--protein-cysteine methyltransferase 23, 150
MMP0084 hypothetical protein MMP0084 49, 106
MMP0113 hypothetical protein MMP0113 23, 75, 142
MMP0115 nitroreductase 2, 23, 159
MMP0239 hypothetical protein MMP0239 1, 49, 75, 106
MMP0268 truA tRNA pseudouridine synthase A 49, 51
MMP0277 TraB family protein 49, 90
MMP0279 mptG beta-ribofuranosylaminobenzene 5'-phosphate synthase family protein 49, 90
MMP0302 hypothetical protein MMP0302 49, 90
MMP0307 hypothetical protein MMP0307 33, 49, 153
MMP0321 hypothetical protein MMP0321 23, 90
MMP0322 rfcB replication factor C large subunit 23, 67
MMP0476 hypothetical protein MMP0476 23, 90
MMP0477 hypothetical protein MMP0477 23, 90
MMP0496 glutamate synthase subunit-related 23, 159
MMP0528 hypothetical protein MMP0528 23, 150
MMP0562 hypothetical protein MMP0562 49, 124
MMP0563 hypothetical protein MMP0563 23, 124
MMP0643 hypothetical protein MMP0643 49, 65
MMP0725 putative integral membrane protein 49, 75, 90, 151
MMP0727 uvrB excinuclease ABC subunit B 49, 142
MMP0742 hypothetical protein MMP0742 23, 49
MMP0799 TetR family transcriptional regulator Member 9, 23
MMP0902 hypothetical protein MMP0902 12, 49, 55
MMP0918 asnB glutamine-hydrolyzing asparagine synthase 49, 115
MMP0997 blue (type1) copper domain-containing protein 23, 43, 90, 125
MMP1019 PEGA domain-containing protein 23, 150
MMP1218 hypothetical protein MMP1218 12, 46, 49
MMP1224 ABC-type amino acid transport/signal transduction systems periplasmic component-related 23, 90
MMP1235 moaE molybdopterin biosynthesis MoaE 49, 55, 106, 117, 150
MMP1282 hypothetical protein MMP1282 49, 102, 106, 150
MMP1283 hypothetical protein MMP1283 49, 102, 150
MMP1290 GTP-binding protein 49, 115
MMP1329 ferredoxin 23, 159
MMP1343 hypothetical protein MMP1343 49, 151
MMP1345 undecaprenyl pyrophospahte synthetase-like protein 49, 111
MMP1346 basic helix-loop-helix dimerization domain-containing protein 49, 67, 142
MMP1372 manB phosphomannomutase 49, 94, 152
MMP1430 cation transporter 49, 115
MMP1431 2pgk 2-phosphoglycerate kinase 49, 51
MMP1551 ffh signal recognition particle protein Srp54 49, 55, 83
MMP1553 rdxA nitroreductase family protein 23, 90, 159
MMP1603 ferredoxin 12, 49
MMP1606 flavoprotein:DNA/pantothenate metabolism flavoprotein 1, 13, 49
MMP1607 hypothetical protein MMP1607 49, 55, 83
Unanno_39 None 23, 33
Unanno_42 None 49, 90
Unanno_52 None 23, 90
Unanno_62 None 49, 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 MMP0742
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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