Part mutual information for quantifying direct associations in networks.

Abstract:

:Quantitatively identifying direct dependencies between variables is an important task in data analysis, in particular for reconstructing various types of networks and causal relations in science and engineering. One of the most widely used criteria is partial correlation, but it can only measure linearly direct association and miss nonlinear associations. However, based on conditional independence, conditional mutual information (CMI) is able to quantify nonlinearly direct relationships among variables from the observed data, superior to linear measures, but suffers from a serious problem of underestimation, in particular for those variables with tight associations in a network, which severely limits its applications. In this work, we propose a new concept, "partial independence," with a new measure, "part mutual information" (PMI), which not only can overcome the problem of CMI but also retains the quantification properties of both mutual information (MI) and CMI. Specifically, we first defined PMI to measure nonlinearly direct dependencies between variables and then derived its relations with MI and CMI. Finally, we used a number of simulated data as benchmark examples to numerically demonstrate PMI features and further real gene expression data from Escherichia coli and yeast to reconstruct gene regulatory networks, which all validated the advantages of PMI for accurately quantifying nonlinearly direct associations in networks.

authors

Zhao J,Zhou Y,Zhang X,Chen L

doi

10.1073/pnas.1522586113

subject

Has Abstract

pub_date

2016-05-03 00:00:00

pages

5130-5

issue

18

eissn

0027-8424

issn

1091-6490

pii

1522586113

journal_volume

113

pub_type

杂志文章
  • Monovalent antibodies directed to transformation-sensitive membrane components inhibit the process of viral transformation.

    abstract::Monovalent antibodies (Fab) directed to two classes of transformation-sensitive cell surface components, ganglioside and galactoprotein a (Gap a), inhibit the process of oncogenic viral transformation of cells. Mouse 3T3 cells infected with murine sarcoma virus were not transformed in terms of morphology change and en...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.75.12.6049

    authors: Lingwood CA,Ng A,Hakomori S

    更新日期:1978-12-01 00:00:00

  • Shear stress activates mitochondrial oxidative phosphorylation by reducing plasma membrane cholesterol in vascular endothelial cells.

    abstract::Vascular endothelial cells (ECs) sense and respond to hemodynamic shear stress, which is critical for circulatory homeostasis and the pathophysiology of vascular diseases. The mechanisms of shear stress mechanotransduction, however, remain elusive. We previously demonstrated a direct role of mitochondria in the purine...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.2014029117

    authors: Yamamoto K,Nogimori Y,Imamura H,Ando J

    更新日期:2020-12-29 00:00:00

  • Evidence for secretory pathway localization of a voltage-dependent anion channel isoform.

    abstract::Voltage-dependent anion channels (VDACs) are pore-forming proteins (porins) that form the major pathway for movement of adenine nucleotides through the outer mitochondrial membrane. Electrophysiological studies indicate that VDAC-like channel activity is also prevalent in the cell membranes of many mammalian cells. Ho...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.060242297

    authors: Buettner R,Papoutsoglou G,Scemes E,Spray DC,Dermietzel R

    更新日期:2000-03-28 00:00:00

  • AKAP220 manages apical actin networks that coordinate aquaporin-2 location and renal water reabsorption.

    abstract::Filtration through the kidney eliminates toxins, manages electrolyte balance, and controls water homeostasis. Reabsorption of water from the luminal fluid of the nephron occurs through aquaporin-2 (AQP2) water pores in principal cells that line the kidney-collecting duct. This vital process is impeded by formation of ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1607745113

    authors: Whiting JL,Ogier L,Forbush KA,Bucko P,Gopalan J,Seternes OM,Langeberg LK,Scott JD

    更新日期:2016-07-26 00:00:00

  • Isolation and primary structure of tumor-derived peptides related to human pancreastatin and chromogranin A.

    abstract::Using an antiserum raised against a synthetic C-terminal peptide of porcine pancreastatin, we detected pancreastatin-like immunoreactivity (PLI) in human pancreatic islets, adrenal medulla, and endocrine tumors. From a carcinoid liver metastasis, human PLI was extracted and purified by HPLC. Two C-terminally amidated ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.85.21.8231

    authors: Schmidt WE,Siegel EG,Kratzin H,Creutzfeldt W

    更新日期:1988-11-01 00:00:00

  • A novel amplicon at 8p22-23 results in overexpression of cathepsin B in esophageal adenocarcinoma.

    abstract::Cathepsin B (CTSB) is overexpressed in tumors of the lung, prostate, colon, breast, and stomach. However, evidence of primary genomic alterations in the CTSB gene during tumor initiation or progression has been lacking. We have found a novel amplicon at 8p22-23 that results in CTSB overexpression in esophageal adenoca...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.95.21.12410

    authors: Hughes SJ,Glover TW,Zhu XX,Kuick R,Thoraval D,Orringer MB,Beer DG,Hanash S

    更新日期:1998-10-13 00:00:00

  • Modifiers of free radicals inhibit in vitro the oncogenic actions of x-rays, bleomycin, and the tumor promoter 12-O-tetradecanoylphorbol 13-acetate.

    abstract::Using short-term cultures of hamster embryo cells, we have examined the effects of the free-radical scavenger superoxide dismutase (superoxide:superoxide oxidoreductase, EC 1.15.1.1) and the enzyme catalase (hydrogen-peroxide:hydrogenperoxide oxidoreductase, EC 1.11.1.6) on x-ray- and bleomycin-induced transformation ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.5.1304

    authors: Borek C,Troll W

    更新日期:1983-03-01 00:00:00

  • Analogues of diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A) as potential anti-platelet-aggregation agents.

    abstract::Dense granules of platelets contain a high content of diadenosine 5',5'''-P1,P4-tetraphosphate (Ap4A). We have previously demonstrated an antithrombotic effect of this compound in a live rabbit model. In the present study we find that certain synthetic Ap4A analogues are superior to Ap4A in inhibiting ADP-induced aggr...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.89.6.2370

    authors: Zamecnik PC,Kim B,Gao MJ,Taylor G,Blackburn GM

    更新日期:1992-03-15 00:00:00

  • Computation of large molecules with the hartree-fock model.

    abstract::The usual way to compute Hartree-Fock type functions for molecules is by an expansion of the one-electron functions (molecular orbitals) in a linear combination of analytical functions (LCAO-MO-SCF, linear combination of atomic orbitals-Molecular Orbital-Self Consistent field). The expansion coefficients are obtained ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.69.10.2942

    authors: Clementi E

    更新日期:1972-10-01 00:00:00

  • Opiate receptor knockout mice define mu receptor roles in endogenous nociceptive responses and morphine-induced analgesia.

    abstract::Morphine produces analgesia at opiate receptors expressed in nociceptive circuits. mu, delta, and kappa opiate receptor subtypes are expressed in circuits that can modulate nociception and receive inputs from endogenous opioid neuropeptide ligands. The roles played by each receptor subtype in nociceptive processing in...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.4.1544

    authors: Sora I,Takahashi N,Funada M,Ujike H,Revay RS,Donovan DM,Miner LL,Uhl GR

    更新日期:1997-02-18 00:00:00

  • WNT/RYK signaling restricts goblet cell differentiation during lung development and repair.

    abstract::Goblet cell metaplasia and mucus hypersecretion are observed in many pulmonary diseases, including asthma, chronic obstructive pulmonary disease (COPD), and cystic fibrosis. However, the regulation of goblet cell differentiation remains unclear. Here, we identify a regulator of this process in an N-ethyl-N-nitrosourea...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1911071116

    authors: Kim HT,Yin W,Nakamichi Y,Panza P,Grohmann B,Buettner C,Guenther S,Ruppert C,Kobayashi Y,Guenther A,Stainier DYR

    更新日期:2019-12-17 00:00:00

  • Recommending teams promotes prosocial lending in online microfinance.

    abstract::This paper reports the results of a large-scale field experiment designed to test the hypothesis that group membership can increase participation and prosocial lending for an online crowdlending community, Kiva. The experiment uses variations on a simple email manipulation to encourage Kiva members to join a lending t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1606085113

    authors: Ai W,Chen R,Chen Y,Mei Q,Phillips W

    更新日期:2016-12-27 00:00:00

  • Expression in Escherichia coli of chemically synthesized genes for human insulin.

    abstract::Synthetic genes for human insulin A and B chains were cloned separately in plasmid pBR322. The cloned synthetic genes were then fused to an Escherichia coli beta-galactosidase gene to provide efficient transcription and translation and a stable precursor protein. The insulin peptides were cleaved from beta-galactosida...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.76.1.106

    authors: Goeddel DV,Kleid DG,Bolivar F,Heyneker HL,Yansura DG,Crea R,Hirose T,Kraszewski A,Itakura K,Riggs AD

    更新日期:1979-01-01 00:00:00

  • REM sleep in naps differentially relates to memory consolidation in typical preschoolers and children with Down syndrome.

    abstract::Sleep is recognized as a physiological state associated with learning, with studies showing that knowledge acquisition improves with naps. Little work has examined sleep-dependent learning in people with developmental disorders, for whom sleep quality is often impaired. We examined the effect of natural, in-home naps ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1811488115

    authors: Spanò G,Gómez RL,Demara BI,Alt M,Cowen SL,Edgin JO

    更新日期:2018-11-13 00:00:00

  • UV excitation of single DNA and RNA strands produces high yields of exciplex states between two stacked bases.

    abstract::Excited electronic states created by UV excitation of the diribonucleoside monophosphates ApA, ApG, ApC, ApU, and CpG were studied by the femtosecond transient-absorption technique. Bleach recovery signals recorded at 252 nm show that long-lived excited states are formed in all five dinucleosides. The lifetimes of the...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0802079105

    authors: Takaya T,Su C,de La Harpe K,Crespo-Hernández CE,Kohler B

    更新日期:2008-07-29 00:00:00

  • Nonsense mutations affecting the his4 enzyme complex of yeast.

    abstract::The his4 region of yeast contains the information necessary for the catalysis of three steps in the histidine biosynthetic pathway. The three activities specified by this region remain physically associated during gel filtration and ultracentrifugation and after extensive purification. Nonsense mutations in the "opera...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.63.4.1198

    authors: Shaffer B,Rytka J,Fink GR

    更新日期:1969-08-01 00:00:00

  • Direct photoaffinity labeling of tubulin with colchicine.

    abstract::Ultraviolet irradiation of the [3H]colchicine-tubulin complex leads to direct photolabeling of tubulin with low but practicable efficiency. The bulk (70% to greater than 90%) of the labeling occurs on beta-tubulin and appears early after irradiation, whereas alpha-tubulin is labeled later. The labeling ratio of beta-t...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.88.7.2820

    authors: Wolff J,Knipling L,Cahnmann HJ,Palumbo G

    更新日期:1991-04-01 00:00:00

  • Antibodies against membrane interleukin 1 alpha activate accessory cells to stimulate proliferation of T lymphocytes.

    abstract::Some monoclonal antibodies (mAbs) against interleukin (IL) 1 alpha have been found to activate antigen-presenting cells (APC, human peripheral blood monocytes and B lymphocytes), so that unstimulated T lymphocytes cultured with them are induced to proliferate and secrete IL-2. Control mAbs of the same isotypes and mAb...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.87.4.1305

    authors: Eugui EM,Almquist SJ

    更新日期:1990-02-01 00:00:00

  • Phase competition in trisected superconducting dome.

    abstract::A detailed phenomenology of low energy excitations is a crucial starting point for microscopic understanding of complex materials, such as the cuprate high-temperature superconductors. Because of its unique momentum-space discrimination, angle-resolved photoemission spectroscopy (ARPES) is ideally suited for this task...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1209471109

    authors: Vishik IM,Hashimoto M,He RH,Lee WS,Schmitt F,Lu D,Moore RG,Zhang C,Meevasana W,Sasagawa T,Uchida S,Fujita K,Ishida S,Ishikado M,Yoshida Y,Eisaki H,Hussain Z,Devereaux TP,Shen ZX

    更新日期:2012-11-06 00:00:00

  • Stepwise proteolysis liberates tau fragments that nucleate the Alzheimer-like aggregation of full-length tau in a neuronal cell model.

    abstract::Tau is a highly soluble protein, yet it aggregates abnormally in Alzheimer's disease. Here, we address the question of proteolytic processing of tau and the nucleation of aggregates by tau fragments. We show in neuronal cell models that fragments of the repeat domain of tau containing mutations of FTDP17 (frontotempor...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0703676104

    authors: Wang YP,Biernat J,Pickhardt M,Mandelkow E,Mandelkow EM

    更新日期:2007-06-12 00:00:00

  • Chromosome 14 transfer and functional studies identify a candidate tumor suppressor gene, mirror image polydactyly 1, in nasopharyngeal carcinoma.

    abstract::Chromosome 14 allelic loss is common in nasopharyngeal carcinoma (NPC) and may reflect essential tumor suppressor gene loss in tumorigenesis. An intact chromosome 14 was transferred to an NPC cell line using a microcell-mediated chromosome transfer approach. Microcell hybrids (MCHs) containing intact exogenously trans...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0900198106

    authors: Cheung AK,Lung HL,Ko JM,Cheng Y,Stanbridge EJ,Zabarovsky ER,Nicholls JM,Chua D,Tsao SW,Guan XY,Lung ML

    更新日期:2009-08-25 00:00:00

  • Handoff from recombinase to replisome: insights from transposition.

    abstract::Bacteriophage Mu replicates as a transposable element, exploiting host enzymes to promote initiation of DNA synthesis. The phage-encoded transposase MuA, assembled into an oligomeric transpososome, promotes transfer of Mu ends to target DNA, creating a fork at each end, and then remains tightly bound to both forks. In...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章,评审

    doi:10.1073/pnas.111007898

    authors: Nakai H,Doseeva V,Jones JM

    更新日期:2001-07-17 00:00:00

  • A gastrolith protein serving a dual role in the formation of an amorphous mineral containing extracellular matrix.

    abstract::Despite the proclamation of Lowenstam and Weiner that crustaceans are the "champions of mineral mobilization and deposition of the animal kingdom," relatively few proteins from the two main calcification sites in these animals, i.e., the exoskeleton and the transient calcium storage organs, have been identified, seque...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0800193105

    authors: Shechter A,Glazer L,Cheled S,Mor E,Weil S,Berman A,Bentov S,Aflalo ED,Khalaila I,Sagi A

    更新日期:2008-05-20 00:00:00

  • Docosahexaenoic acid is a strong inhibitor of prostaglandin but not leukotriene biosynthesis.

    abstract::Docosahexaenoic acid (DCHA), a major polyunsaturated acid component of fish lipid, is not a substrate for prostaglandin synthetase from ram seminal vesicles but is a strong competitive inhibitor (Ki, 0.36 microM) of the conversion by this enzyme of arachidonate (Km, 5.9 microM) to prostaglandins. In contrast, DCHA exh...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.12.3581

    authors: Corey EJ,Shih C,Cashman JR

    更新日期:1983-06-01 00:00:00

  • Quantitative correlation of homogeneously stained regions on chromosome 10 with dihydrofolate reductase enzyme in human cells.

    abstract::Gene amplification may be visualized within a chromosome as a homogeneously stained region (HSR) and HSRs have rarely been reported in human tumor cells with identification of the amplified gene. A parental line and seven clones derived from KB cells resistant to methotrexate (MTX) contain dihydrofolate reductase (DHF...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.80.3.807

    authors: Wolman SR,Craven ML,Grill SP,Domin BA,Cheng YC

    更新日期:1983-02-01 00:00:00

  • Disrupted synaptic development in the hypoxic newborn brain.

    abstract::Infants born prematurely risk significant life-long cognitive disability, representing a major pediatric health crisis. The neuropathology of this cohort is accurately modeled in mice subjected to sublethal postnatal hypoxia. Massively parallel transcriptome analysis using cDNA microchips (9,262 genes), combined with ...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.232568799

    authors: Curristin SM,Cao A,Stewart WB,Zhang H,Madri JA,Morrow JS,Ment LR

    更新日期:2002-11-26 00:00:00

  • Absence of detectable IgM in enzymatically or biosynthetically labeled thymus-derived lymphocytes.

    abstract::Surface proteins of mouse thymus and spleen cells were radioiodinated with lactoperoxidase. After solubilization, the labeled proteins were precipitated by antibodies directed against mouse immunoglobulin chains; the precipitates were analyzed by radioautography after Na dodecyl sulfate-gel electrophoresis. Radioactiv...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.70.10.2879

    authors: Lisowska-Bernstein B,Rinuy A,Vassalli P

    更新日期:1973-10-01 00:00:00

  • Vinpocetine inhibits NF-kappaB-dependent inflammation via an IKK-dependent but PDE-independent mechanism.

    abstract::Inflammation is a hallmark of many diseases, such as atherosclerosis, chronic obstructive pulmonary disease, arthritis, infectious diseases, and cancer. Although steroids and cyclooxygenase inhibitors are effective antiinflammatory therapeutical agents, they may cause serious side effects. Therefore, developing unique...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.0914414107

    authors: Jeon KI,Xu X,Aizawa T,Lim JH,Jono H,Kwon DS,Abe J,Berk BC,Li JD,Yan C

    更新日期:2010-05-25 00:00:00

  • Floodplains as an Achilles' heel of Amazonian forest resilience.

    abstract::The massive forests of central Amazonia are often considered relatively resilient against climatic variation, but this view is challenged by the wildfires invoked by recent droughts. The impact of such fires that spread from pervasive sources of ignition may reveal where forests are less likely to persist in a drier f...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.1617988114

    authors: Flores BM,Holmgren M,Xu C,van Nes EH,Jakovac CC,Mesquita RCG,Scheffer M

    更新日期:2017-04-25 00:00:00

  • Recombination activities of HsDmc1 protein, the meiotic human homolog of RecA protein.

    abstract::Meiosis-specific homologs of RecA protein have been identified in Saccharomyces cerevisiae and higher eukaryotes including mammals, but their enzymatic activities have not been described. We have purified the human protein HsDmc1 produced in Escherichia coli from a cloned copy of the cDNA. The recombinant enzyme had D...

    journal_title:Proceedings of the National Academy of Sciences of the United States of America

    pub_type: 杂志文章

    doi:10.1073/pnas.94.21.11221

    authors: Li Z,Golub EI,Gupta R,Radding CM

    更新日期:1997-10-14 00:00:00