Data integration with STRING

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Lars Juhl Jensen

The document discusses data integration strategies used by STRING, a database of known and predicted protein-protein interactions. STRING combines interaction data from numerous sources like experimental repositories, curated databases, text mining, and computational prediction methods. It maps identifiers across different databases, assigns confidence scores to interactions, and provides an interactive web interface for users to access and explore the integrated interaction network. External groups can contribute additional interaction data to STRING by hosting their own public data servers or providing data files in specified formats.

Sciences Technologie

Data integration with STRING
Lars Juhl Jensen

association networks

guilt by association

molecular networks

proteins

string-db.org

small molecules

stitch-db.org

non-coding RNAs

data integration

computational predictions

gene neighborhood

Korbel et al., Nature Biotechnology, 2004

experimental data

gene expression

curated knowledge

pathways

Letunic & Bork, Trends in Biochemical Sciences, 2008

many databases

different formats

different identifiers

variable quality

not comparable

hard work

(Ph.D. students)

common identifiers

quality scores

von Mering et al., Nucleic Acids Research, 2005

score calibration

von Mering et al., Nucleic Acids Research, 2005

homology-based transfer

Franceschini et al., Nucleic Acids Research, 2013

missing most of the data

text mining

>10 km

too much to read

computer

as smart as a dog

teach it specific tricks

named entity recognition

comprehensive lexicon

CDC2

cyclin dependent kinase 1

flexible matching

upper- and lower-case

CDC2

Cdc2

spaces and hyphens

cyclin dependent kinase 1

cyclin-dependent kinase 1

name expansions

prefixes and postfixes

CDC2

hCDC2

“black list”

SDS

co-mentioning

counting

within documents

within paragraphs

within sentences

external data

payload mechanism

extra data on nodes

colored halos

text in node popup

URL in node popup

new nodes

ncRNAs

new edges

evidence type

evidence score

text in edge popup

URL in edge popup

legend

you host the data

user accesses STRING

STRING gets data from you

your server must be public

restrict access to STRING

JSON configuration file

TSV data files

node data

edge data

extension node data

extension edge data

web services as alternative

big datasets

get only required data

questions?

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En vedette

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En vedette (9)

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Grade 7 - Lesson 1 - Microscope and Its Functions

OrtegaSyrineMay

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300003-World Science Day For Peace And Development.pptx

300003-World Science Day For Peace And Development.pptx

Clean In Place(CIP).pptx .

Clean In Place(CIP).pptx .

Clean In Place(CIP).pptx .

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development of diagnostic enzyme assay to detect leuser virus

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Context. WASP-76 b has been a recurrent subject of study since the detection of a signature in high-resolution transit spectroscopy data indicating an asymmetry between the two limbs of the planet. The existence of this asymmetric signature has been confirmed by multiple studies, but its physical origin is still under debate. In addition, it contrasts with the absence of asymmetry reported in the infrared (IR) phase curve. Aims. We provide a more comprehensive dataset of WASP-76 b with the goal of drawing a complete view of the physical processes at work in this atmosphere. In particular, we attempt to reconcile visible high-resolution transit spectroscopy data and IR broadband phase curves. Methods. We gathered 3 phase curves, 20 occultations, and 6 transits for WASP-76 b in the visible with the CHEOPS space telescope. We also report the analysis of three unpublished sectors observed by the TESS space telescope (also in the visible), which represents 34 phase curves. Results. WASP-76 b displays an occultation of 260±11 and 152±10 ppm in TESS and CHEOPS bandpasses respectively. Depending on the composition assumed for the atmosphere and the data reduction used for the IR data, we derived geometric albedo estimates that range from 0.05 ± 0.023 to 0.146 ± 0.013 and from <0.13 to 0.189 ± 0.017 in the CHEOPS and TESS bandpasses, respectively. As expected from the IR phase curves, a low-order model of the phase curves does not yield any detectable asymmetry in the visible either. However, an empirical model allowing for sharper phase curve variations offers a hint of a flux excess before the occultation, with an amplitude of ∼40 ppm, an orbital offset of ∼−30◦ , and a width of ∼20◦ . We also constrained the orbital eccentricity of WASP-76 b to a value lower than 0.0067, with a 99.7% confidence level. This result contradicts earlier proposed scenarios aimed at explaining the asymmetry observed in high-resolution transit spectroscopy. Conclusions. In light of these findings, we hypothesise that WASP-76 b could have night-side clouds that extend predominantly towards its eastern limb. At this limb, the clouds would be associated with spherical droplets or spherically shaped aerosols of an unknown species, which would be responsible for a glory effect in the visible phase curves.

Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b

Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b

Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b

Site Acceptance Test .

Site Acceptance Test .

Site Acceptance Test .

Poonam Aher Patil

COST ESTIMATION FOR A RESEARCH PROJECT.pptx

COST ESTIMATION FOR A RESEARCH PROJECT.pptx

COST ESTIMATION FOR A RESEARCH PROJECT.pptx

FarihaAbdulRasheed

Cotton crops are vulnerable to a variety of sucking pests, which can severely impact plant health, yield, and fiber quality. These pests primarily feed on plant sap, extracting nutrients directly from the plant's vascular system. Here's a breakdown of some of the most significant sucking pests in cotton cultivation: Aphids: Cotton aphids or melon aphids can cause direct damage by sucking sap and indirect damage by secreting honeydew, which encourages sooty mold growth. This can interfere with photosynthesis and weaken the plant. Aphids can also transmit viral diseases. Whiteflies: Two species, the silverleaf whitefly and the bandedwinged whitefly, are particularly troublesome. They not only suck sap from the underside of leaves, causing yellowing and leaf drop, but their honeydew excretion promotes sooty mold and they can transmit several plant viruses. Thrips: While thrips can chew on plants, their primary damage to cotton is through sucking. They attack the cotton plant during its seedling stage, which can stunt growth and reduce vigor. Thrips are also capable of transmitting the Cotton Bud disease. Spider Mites: These are not insects but arachnids. Spider mites, such as the two-spotted spider mite, suck cell contents from the leaves, leading to speckled discoloration and potentially significant leaf loss if infestations are severe. Leafhoppers: Including various species, leafhoppers can cause direct damage through feeding, which results in leaf curling and stunted growth. They can also be vectors for plant diseases. Mealybugs: These pests are less common but can be problematic, especially in clustered planting conditions. They suck sap and secrete honeydew, which leads to sooty mold. Mealybugs can also spread viruses. Stink Bugs: Although primarily known for their chewing mouthparts, certain stink bugs can cause damage similar to sucking pests by injecting saliva into the plant and sucking out nutrients, leading to boll damage and stained lint. Management Strategies: Cultural Controls: This includes practices such as crop rotation, using resistant varieties, and managing planting and harvesting times to avoid peak pest populations. Biological Controls: Beneficial insects like lady beetles, lacewings, and predatory mites can naturally control sucking pest populations. Parasitic wasps also play a role in controlling aphid and whitefly populations. Chemical Controls: Insecticides may be used but should be chosen carefully to minimize resistance development and preserve beneficial insects. Systemic insecticides can be particularly effective against sucking pests. Integrated Pest Management (IPM): Combining multiple control strategies based on monitoring and thresholds to apply the most effective and environmentally sensitive approach. Effective management of sucking pests in cotton requires a thorough understanding of the pest species present, their life cycles, and the ecological balance of the field environment.

Pests of cotton_Sucking_Pests_Dr.UPR.pdf

Pests of cotton_Sucking_Pests_Dr.UPR.pdf

Pests of cotton_Sucking_Pests_Dr.UPR.pdf

Forensic Biology & Its biological significance.pdf

Forensic Biology & Its biological significance.pdf

Forensic Biology & Its biological significance.pdf

rohankumarsinghrore1

Thyroid Physiology_Dr.E. Muralinath_ Associate Professor

Thyroid Physiology_Dr.E. Muralinath_ Associate Professor

Thyroid Physiology_Dr.E. Muralinath_ Associate Professor

Theoretical predictions and observational data indicate a class of sub-Neptune exoplanets may have water-rich interiors covered by hydrogen-dominated atmospheres. Provided suitable climate conditions, such planets could host surface liquid oceans. Motivated by recent JWST observations of K2-18 b, we self-consistently model the photochemistry and potential detectability of biogenic sulfur gases in the atmospheres of temperate sub-Neptune waterworlds for the first time. On Earth today, organic sulfur compounds produced by marine biota are rapidly destroyed by photochemical processes before they can accumulate to significant levels. Domagal-Goldman et al. suggest that detectable biogenic sulfur signatures could emerge in Archean-like atmospheres with higher biological production or low UV flux. In this study, we explore biogenic sulfur across a wide range of biological fluxes and stellar UV environments. Critically, the main photochemical sinks are absent on the nightside of tidally locked planets. To address this, we further perform experiments with a 3D general circulation model and a 2D photochemical model (VULCAN 2D) to simulate the global distribution of biogenic gases to investigate their terminator concentrations as seen via transmission spectroscopy. Our models indicate that biogenic sulfur gases can rise to potentially detectable levels on hydrogen-rich water worlds, but only for enhanced global biosulfur flux (20 times modern Earth’s flux). We find that it is challenging to identify DMS at 3.4 μm where it strongly overlaps with CH4, whereas it is more plausible to detect DMS and companion byproducts, ethylene (C2H4) and ethane (C2H6), in the mid-infrared between 9 and 13 μm. Unified Astronomy Thesaurus concepts: Exoplanet atmospheres (487); Exoplanet

Biogenic Sulfur Gases as Biosignatures on Temperate Sub-Neptune Waterworlds

Biogenic Sulfur Gases as Biosignatures on Temperate Sub-Neptune Waterworlds

Biogenic Sulfur Gases as Biosignatures on Temperate Sub-Neptune Waterworlds

Module for Grade 9 for Asynchronous/Distance learning

Module for Grade 9 for Asynchronous/Distance learning

Module for Grade 9 for Asynchronous/Distance learning

Dernier (20)

Grade 7 - Lesson 1 - Microscope and Its Functions

Grade 7 - Lesson 1 - Microscope and Its Functions

Grade 7 - Lesson 1 - Microscope and Its Functions

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300003-World Science Day For Peace And Development.pptx

300003-World Science Day For Peace And Development.pptx

Clean In Place(CIP).pptx .

Clean In Place(CIP).pptx .

Clean In Place(CIP).pptx .

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development of diagnostic enzyme assay to detect leuser virus

development of diagnostic enzyme assay to detect leuser virus

development of diagnostic enzyme assay to detect leuser virus

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Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b

Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b

Asymmetry in the atmosphere of the ultra-hot Jupiter WASP-76 b

Site Acceptance Test .

Site Acceptance Test .

Site Acceptance Test .

COST ESTIMATION FOR A RESEARCH PROJECT.pptx

COST ESTIMATION FOR A RESEARCH PROJECT.pptx

COST ESTIMATION FOR A RESEARCH PROJECT.pptx

Pests of cotton_Sucking_Pests_Dr.UPR.pdf

Pests of cotton_Sucking_Pests_Dr.UPR.pdf

Pests of cotton_Sucking_Pests_Dr.UPR.pdf

Forensic Biology & Its biological significance.pdf

Forensic Biology & Its biological significance.pdf

Forensic Biology & Its biological significance.pdf

Thyroid Physiology_Dr.E. Muralinath_ Associate Professor

Thyroid Physiology_Dr.E. Muralinath_ Associate Professor

Thyroid Physiology_Dr.E. Muralinath_ Associate Professor

Biogenic Sulfur Gases as Biosignatures on Temperate Sub-Neptune Waterworlds

Biogenic Sulfur Gases as Biosignatures on Temperate Sub-Neptune Waterworlds

Biogenic Sulfur Gases as Biosignatures on Temperate Sub-Neptune Waterworlds

Module for Grade 9 for Asynchronous/Distance learning

Module for Grade 9 for Asynchronous/Distance learning

Module for Grade 9 for Asynchronous/Distance learning

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1. Data integration with STRING Lars Juhl Jensen

2. association networks

3. guilt by association

4.

5. molecular networks

7. string-db.org

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9. stitch-db.org

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