Organism : Methanococcus maripaludis S2 | Module List :
MMP1347 HMmB

histone B

CircVis
Functional Annotations (5)
Function System
Histones H3 and H4 cog/ cog
intracellular go/ cellular_component
nucleus go/ cellular_component
transcription initiation factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
GeneModule member RegulatorRegulator MotifMotif

Cytoscape Web
Regulation information for MMP1347
(Mouseover regulator name to see its description)

MMP1347 is regulated by 4 influences and regulates 5 modules.
Regulators for MMP1347 HMmB (4)
Regulator Module Operator
H2 123 ef
MMP0052
MMP0480
123 combiner
MMP0086
MMP0097
123 combiner
MMP0097
MMP0527
123 combiner

Warning: MMP1347 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
723 7.00e-06 gggGG.Gt
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724 5.10e+02 TGAcTGAgTAGTCAaTCTTA
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899 1.50e+03 TGaGacACatCgGc.G
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900 4.60e+03 TtGAatTTaAAAc
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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 MMP1347

MMP1347 is enriched for 5 functions in 3 categories.
Enrichment Table (5)
Function System
Histones H3 and H4 cog/ cog
intracellular go/ cellular_component
nucleus go/ cellular_component
transcription initiation factor activity go/ molecular_function
sequence-specific DNA binding go/ molecular_function
Module neighborhood information for MMP1347

MMP1347 has total of 63 gene neighbors in modules 31, 123
Gene neighbors (63)
Gene Common Name Description Module membership
Antisense_12 None 31, 119
Antisense_28 None 31, 37
MMP0020 nickel responsive regulator 49, 123
MMP0123 purT phosphoribosylglycinamide formyltransferase 2 50, 123
MMP0194 hypothetical protein MMP0194 31, 108, 131
MMP0195 hypothetical protein MMP0195 6, 31
MMP0198 ABC-type iron(III) transport system ATP binding protein 26, 31, 82
MMP0208 hypothetical protein MMP0208 26, 31, 42, 82
MMP0375 radical SAM domain-containing protein 31, 45
MMP0435 hypothetical protein MMP0435 31, 72
MMP0436 rimK RimK domain-containing protein 6, 31, 42, 72, 82, 110
MMP0437 hypothetical protein MMP0437 6, 31, 42, 53, 82
MMP0473 hypothetical protein MMP0473 31, 42
MMP0474 hypothetical protein MMP0474 31, 131
MMP0475 hypothetical protein MMP0475 26, 31, 45, 72, 82, 151
MMP0484 sodium/hydrogen exchanger 31, 72, 127, 131, 161
MMP0495 hypothetical protein MMP0495 31, 42, 127, 155
MMP0501 hypothetical protein MMP0501 31, 82
MMP0519 hypothetical protein MMP0519 6, 31, 161
MMP0624 hypothetical protein MMP0624 50, 123
MMP0628 TOBE domain-containing protein 108, 123, 156
MMP0673 hypothetical protein MMP0673 5, 31
MMP0683 ftsY signal recognition particle-docking protein FtsY 50, 123
MMP0740 purine NTPase 6, 26, 31, 72, 82
MMP0763 hypothetical protein MMP0763 43, 123
MMP0772 hypothetical protein MMP0772 42, 123
MMP0778 hypothetical protein MMP0778 31, 72
MMP0779 hypothetical protein MMP0779 31, 72
MMP0782 hypothetical protein MMP0782 31, 53, 72, 127, 155, 161
MMP0801 hypothetical protein MMP0801 31, 72
MMP0802 Iron-containing alcohol dehydrogenase 31, 53
MMP0820 frcA coenzyme F420-reducing hydrogenase subunit alpha 123, 131
MMP0825 hdrA heterodisulfide reductase subunit A 45, 123
MMP0826 hypothetical protein MMP0826 31, 154
MMP0908 CBS domain-containing protein 45, 123
MMP0998 hypothetical protein MMP0998 31, 131
MMP1016 putative CBS domain-containing signal transduction protein 13, 123
MMP1067 succinate dehydrogenase/fumarate reductase iron-sulfur subunit 19, 123
MMP1088 group 1 glycosyl transferase 31, 117
MMP1110 hypothetical protein MMP1110 31, 146
MMP1134 type A flavoprotein 58, 123
MMP1135 flavodoxin:beta-lactamase-like 58, 123
MMP1136 rubrerythrin 58, 123
MMP1154 hdrC1 heterosulfide reductase subunit C1 74, 84, 123
MMP1156 carboxymuconolactone decarboxylase 74, 84, 108, 123
MMP1158 hypothetical protein MMP1158 74, 84, 123
MMP1172 DNA protection protein DPS 6, 31, 82
MMP1223 hypothetical protein MMP1223 19, 123
MMP1229 FUN14 family protein 58, 123
MMP1251 putative CBS domain-containing signal transduction protein 123, 145
MMP1252 CBS domain-containing protein 123, 145
MMP1347 HMmB histone B 31, 123
MMP1439 cofactor-independent phosphoglycerate mutase 58, 123
MMP1533 hypothetical protein MMP1533 13, 123
MMP1534 hypothetical protein MMP1534 13, 123
MMP1596 hypothetical protein MMP1596 31, 42, 155
MMP1642 ATP/GTP-binding motif-containing protein 9, 123
MMP1660 hypothetical protein MMP1660 42, 108, 123, 131
MMP1661 hypothetical protein MMP1661 123, 131
MMP1685 hypothetical protein MMP1685 123, 131
MMP1697 hdrA heterodisulfide reductase subunit A 113, 114, 123
Unanno_32 None 65, 123
Unanno_38 None 45, 123
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 MMP1347
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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