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36-398: The origin of the database was an early data collection published 1988. The first version that was released under the name TRANSFAC was developed at the former German National Research Centre for Biotechnology and designed for local installation (now: Helmholtz Centre for Infection Research ). In one of the first publicly funded bioinformatics projects, launched in 1993, TRANSFAC developed into

72-474: A Helmholtz Center and a university (the institutes are not members of the Helmholtz Association themselves). Examples of Helmholtz Institutes include: The works of the centers are categorised into programmes, which are divided into six research groups. The Helmholtz centers are grouped according to which research group they belong to: Eight of the above-mentioned Helmholtz centers are part of

108-606: A TF to a genomic site is documented by specifying the localization of the site, its sequence and the experimental method applied. All sites that refer to one TF, or a group of closely related TFs, are aligned and used to construct a position-specific scoring matrix (PSSM), or count matrix. Many matrices of the TRANSFAC matrix library have been constructed by a team of curators , others were taken from scientific publications. The TRANSFAC database can be used as an encyclopedia of eukaryotic transcription factors. The target sequences and

144-709: A moon of Saturn, and Triton , a moon of Neptune, have atmospheres mainly of nitrogen . When in the part of its orbit closest to the Sun, Pluto has an atmosphere of nitrogen and methane similar to Triton's, but these gases are frozen when it is farther from the Sun. Other bodies within the Solar System have extremely thin atmospheres not in equilibrium. These include the Moon ( sodium gas), Mercury (sodium gas), Europa (oxygen), Io ( sulfur ), and Enceladus ( water vapor ). The first exoplanet whose atmospheric composition

180-508: A planet from atmospheric escape and that for some magnetizations the presence of a magnetic field works to increase the escape rate. Other mechanisms that can cause atmosphere depletion are solar wind -induced sputtering, impact erosion, weathering , and sequestration—sometimes referred to as "freezing out"—into the regolith and polar caps . Atmospheres have dramatic effects on the surfaces of rocky bodies. Objects that have no atmosphere, or that have only an exosphere, have terrain that

216-525: A resource that became available on the Internet. In 1997, TRANSFAC was transferred to a newly established company, BIOBASE , in order to secure long-term financing of the database. Since then, the most up-to-date version has to be licensed, whereas older versions are free for non-commercial users. Since July 2016, TRANSFAC is maintained and distributed by geneXplain GmbH, Wolfenbüttel, Germany. The content of

252-451: A variable amount of water vapor is also present, on average about 1% at sea level. The low temperatures and higher gravity of the Solar System's giant planets — Jupiter , Saturn , Uranus and Neptune —allow them more readily to retain gases with low molecular masses . These planets have hydrogen–helium atmospheres, with trace amounts of more complex compounds. Two satellites of the outer planets possess significant atmospheres. Titan ,

288-464: A wide range of velocities, there will always be some fast enough to produce a slow leakage of gas into space. Lighter molecules move faster than heavier ones with the same thermal kinetic energy , and so gases of low molecular weight are lost more rapidly than those of high molecular weight. It is thought that Venus and Mars may have lost much of their water when, after being photodissociated into hydrogen and oxygen by solar ultraviolet radiation,

324-423: Is covered in craters . Without an atmosphere, the planet has no protection from meteoroids , and all of them collide with the surface as meteorites and create craters. For planets with a significant atmosphere, most meteoroids burn up as meteors before hitting a planet's surface. When meteoroids do impact, the effects are often erased by the action of wind. Wind erosion is a significant factor in shaping

360-625: Is originally determined by the stellar nebula's chemistry and temperature, but can also by a product processes within the astronomical body outgasing a different atmosphere. The atmospheres of the planets Venus and Mars are principally composed of carbon dioxide and nitrogen , argon and oxygen . The composition of Earth's atmosphere is determined by the by-products of the life that it sustains. Dry air (mixture of gases) from Earth's atmosphere contains 78.08% nitrogen, 20.95% oxygen, 0.93% argon, 0.04% carbon dioxide, and traces of hydrogen, helium, and other "noble" gases (by volume), but generally

396-559: Is promoted through institutional repositories of the individual Helmholtz Centers. To further the idea of open science, the Helmholtz Association maintains the Helmholtz Open Science Coordination Office. Atmosphere An atmosphere (from Ancient Greek ἀτμός ( atmós )  'vapour, steam' and σφαῖρα ( sphaîra )  'sphere') is a layer of gases that envelop an astronomical object , held in place by

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432-401: Is the lowest layer of the atmosphere. This extends from the planetary surface to the bottom of the stratosphere . The troposphere contains 75–80% of the mass of the atmosphere, and is the atmospheric layer wherein the weather occurs; the height of the troposphere varies between 17 km at the equator and 7.0 km at the poles. The stratosphere extends from the top of the troposphere to

468-499: Is used to make nucleotides and amino acids ; plants , algae , and cyanobacteria use carbon dioxide for photosynthesis . The layered composition of the atmosphere minimises the harmful effects of sunlight , ultraviolet radiation, solar wind , and cosmic rays and thus protects the organisms from genetic damage. The current composition of the atmosphere of the Earth is the product of billions of years of biochemical modification of

504-761: The Helmholtz Climate Initiative Regional Climate (in German: Regionale Klimainitiative ) REKLIM in order to tackle the interactions between atmosphere , sea ice , ocean and land surfaces. These interactions determine the climate of the Earth . Detailed observations and process studies are combined within the initiative. For the funding period 2009-2013 the REKLIM-initiative has a budget of 32.2 million Euro. In this funding period,

540-596: The gravity of the object. A planet retains an atmosphere when the gravity is great and the temperature of the atmosphere is low. A stellar atmosphere is the outer region of a star, which includes the layers above the opaque photosphere ; stars of low temperature might have outer atmospheres containing compound molecules . The atmosphere of Earth is composed of nitrogen (78%), oxygen (21%), argon (0.9%), carbon dioxide (0.04%) and trace gases. Most organisms use oxygen for respiration ; lightning and bacteria perform nitrogen fixation which produces ammonia that

576-477: The paleoatmosphere by living organisms. Atmospheres are clouds of gas bound to and engulfing an astronomical focal point of sufficiently dominating mass , adding to its mass, possibly escaping from it or collapsing into it. Because of the latter, such planetary nucleus can develop from interstellar molecular clouds or protoplanetary disks into rocky astronomical objects with varyingly thick atmospheres, gas giants or fusors . Composition and thickness

612-552: The Association is "solving the grand challenges of science, society and industry". Scientists at Helmholtz therefore focus research on complex systems which affect human life and the environment. The namesake of the association is the German physiologist and physicist Hermann von Helmholtz . The annual budget of the Helmholtz Association amounts to €5.8 billion, of which about 70% is raised from public funds. The remaining 30% of

648-529: The TF-target gene relations documented in TRANSFAC were used to construct and analyze transcription regulatory networks. By far the most frequent use of TRANSFAC is the computational prediction of potential TFBS. A number of algorithms exist which either use the individual binding sites or the matrix library for this purpose: Comparison of matrices with the matrix library of TRANSFAC and other sources: A number of servers provide genomic annotations computed with

684-479: The aid of TRANSFAC. Others have used such analyses to infer target gene sets. Helmholtz Association of German Research Centres The Helmholtz Association of German Research Centres ( German : Helmholtz-Gemeinschaft Deutscher Forschungszentren ) is the largest scientific organisation in Germany . It is a union of 18 scientific-technical and biological-medical research centers . The official mission of

720-438: The atmosphere can transport thermal energy from the higher temperature interior up to the surface. From the perspective of a planetary geologist , the atmosphere acts to shape a planetary surface. Wind picks up dust and other particles which, when they collide with the terrain, erode the relief and leave deposits ( eolian processes). Frost and precipitations , which depend on the atmospheric composition, also influence

756-411: The base of the exosphere at 690 km and contains the ionosphere , where solar radiation ionizes the atmosphere. The density of the ionosphere is greater at short distances from the planetary surface in the daytime and decreases as the ionosphere rises at night-time, thereby allowing a greater range of radio frequencies to travel greater distances. The exosphere begins at 690 to 1,000 km from

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792-428: The bottom of the mesosphere , and contains the ozone layer , at an altitude between 15 km and 35 km. It is the atmospheric layer that absorbs most of the ultraviolet radiation that Earth receives from the Sun. The mesosphere ranges from 50 km to 85 km and is the layer wherein most meteors are incinerated before reaching the surface. The thermosphere extends from an altitude of 85 km to

828-569: The budget is acquired by the 19 individual Helmholtz Centres in the form of contract funding. The public funds are provided by the federal government (90%) and the rest by the States of Germany (10%). The Helmholtz Association was ranked #6 in 2022 by the Nature Index , which measures the largest contributors to papers published in 82 leading journals. Members of the Helmholtz Association are: Helmholtz Institutes are partnerships between

864-405: The database is organized in a way that it is centered around the interaction between transcription factors (TFs) and their DNA binding sites (TFBS). TFs are described with regard to their structural and functional features, extracted from the original scientific literature. They are classified to families, classes and superclasses according to the features of their DNA binding domains . Binding of

900-426: The diminishing mass of the gas above the point of barometric measurement. The units of air pressure are based upon the standard atmosphere (atm), which is 101,325  Pa (equivalent to 760  Torr or 14.696  psi ). The height at which the atmospheric pressure declines by a factor of e (an irrational number equal to 2.71828) is called the scale height ( H ). For an atmosphere of uniform temperature,

936-431: The distance from the Sun determines the energy available to heat atmospheric gas to the point where some fraction of its molecules' thermal motion exceed the planet's escape velocity , allowing those to escape a planet's gravitational grasp. Thus, distant and cold Titan , Triton , and Pluto are able to retain their atmospheres despite their relatively low gravities. Since a collection of gas molecules may be moving at

972-442: The hydrogen escaped. Earth's magnetic field helps to prevent this, as, normally, the solar wind would greatly enhance the escape of hydrogen. However, over the past 3 billion years Earth may have lost gases through the magnetic polar regions due to auroral activity, including a net 2% of its atmospheric oxygen. The net effect, taking the most important escape processes into account, is that an intrinsic magnetic field does not protect

1008-406: The past. The circulation of the atmosphere occurs due to thermal differences when convection becomes a more efficient transporter of heat than thermal radiation . On planets where the primary heat source is solar radiation, excess heat in the tropics is transported to higher latitudes. When a planet generates a significant amount of heat internally, such as is the case for Jupiter , convection in

1044-528: The program is divided into seven topics, each of the topics is organized in various work-packages. In the second funding period (2011–2015), three additional topics have been added. The Helmholtz Association was one of the initial signatories of the 2003 Berlin Declaration on Open Access to Knowledge in the Sciences and Humanities . This commitment towards open access publishing of scientific research

1080-501: The regulated genes can be listed for each TF, which can be used as benchmark for TFBS recognition tools or as training sets for new transcription factor binding sites (TFBS) recognition algorithms. The TF classification enables to analyze such data sets with regard to the properties of the DNA-binding domains. Another application is to retrieve all TFs that regulate a given (set of) gene(s). In the context of systems-biological studies,

1116-416: The relief. Climate changes can influence a planet's geological history. Conversely, studying the surface of the Earth leads to an understanding of the atmosphere and climate of other planets. For a meteorologist , the composition of the Earth's atmosphere is a factor affecting the climate and its variations. For a biologist or paleontologist , the Earth's atmospheric composition is closely dependent on

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1152-468: The scale height is proportional to the atmospheric temperature and is inversely proportional to the product of the mean molecular mass of dry air, and the local acceleration of gravity at the point of barometric measurement. Surface gravity differs significantly among the planets. For example, the large gravitational force of the giant planet Jupiter retains light gases such as hydrogen and helium that escape from objects with lower gravity. Secondly,

1188-413: The surface, and extends to roughly 10,000 km, where it interacts with the magnetosphere of Earth. Atmospheric pressure is the force (per unit-area) perpendicular to a unit-area of planetary surface, as determined by the weight of the vertical column of atmospheric gases. In said atmospheric model, the atmospheric pressure , the weight of the mass of the gas, decreases at high altitude because of

1224-417: The terrain of rocky planets with atmospheres, and over time can erase the effects of both craters and volcanoes . In addition, since liquids cannot exist without pressure, an atmosphere allows liquid to be present at the surface, resulting in lakes , rivers and oceans . Earth and Titan are known to have liquids at their surface and terrain on the planet suggests that Mars had liquid on its surface in

1260-461: Was determined is HD 209458b , a gas giant with a close orbit around a star in the constellation Pegasus . Its atmosphere is heated to temperatures over 1,000 K, and is steadily escaping into space. Hydrogen, oxygen, carbon and sulfur have been detected in the planet's inflated atmosphere. The atmosphere of Earth is composed of layers with different properties, such as specific gaseous composition, temperature, and pressure. The troposphere

1296-640: Was then formally approved by its Assembly of Members, an assembly of the directors of the Helmholtz Centers. In a September 2004 Resolution the Assembly adopted the following commitment: "Publications from the Helmholtz Association shall in future, without exception, be available free of charge, as far as no conflicting agreement with publishers or others exists." While the Helmholtz Association has no strict open access mandate. The Helmholtz Association encourages gold open access , while green open access

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