Biomedical subjects

Wei Li

Publications and source records attributed to Wei Li.

At least 91 records · Page 5Linked to original sources

PubMed2006

Reversible immobilization of proteins with streptavidin affinity tags on a surface plasmon resonance biosensor chip.

Dissociation of biotin from streptavidin is very difficult due to their high binding affinity. The re-use of streptavidin-modified surfaces is therefore almost impossible, making devices containing them (e.g. surface plasmon resonance (SPR) sensor chips) expensive. This paper describes a new protocol for reversible and site-directed immobilization of proteins with streptavidin affinity tags on the streptavidin-coated SPR biosensor chip (SA chip). Two streptavidin affinity tags, nano-tag and streptavidin-binding peptide (SBP tag), were applied. They both can specifically interact with streptavidin but have weaker binding force compared to the biotin-streptavidin system, thus allowing association and dissociation under controlled conditions. The SA chip surface could be regenerated repeatedly without loss of activity by injection of 50 mM NaOH solution. The fusion construct of a SBP tag and a single-chain antibody to mature bovine prion protein (scFv-Z186-SBP) interacts with the SA chip, resulting in a single-chain-antibody-modified surface. The chip showed kinetic response to the prion antigen with equilibrium dissociation constant K (D) approximately equal to 4.01 x 10(-7). All results indicated that the capture activity of the SA chip has no irreversible loss after repeated immobilization and regeneration cycles. The method should be of great benefit to various biosensors, biochips and immunoassay applications based on the streptavidin capture surface.

Animals↗

PubMed2006

Discovery of antiglioma activity of biaryl 1,2,3,4-tetrahydroisoquinoline derivatives and conformationally flexible analogues.

Cultured rat astrocytes and C6 rat glioma were used as a differential screen for a variety of 1,2,3,4-tetrahydroisoquinoline (THI) derivatives. Compound 1 [1-(biphenyl-4-ylmethyl)-1,2,3,4-tetrahydroisoquinoline-6,7-diol hydrochloride] selectively blocked the growth of C6 glioma leaving normal astrocytes relatively unaffected. The potential for clinical utility of 1 was further substantiated in human gliomas and other tumor cell lines. Preliminary SAR of this activity was characterized by synthesis and testing of several THI and conformationally flexible variants.

Animals↗

PubMed2006

Auditory cortical responses evoked by pure tones in healthy and sensorineural hearing loss subjects: functional MRI and magnetoencephalography.

BACKGROUND: Blood oxygen level dependent functional magnetic resonance imaging (fMRI) and magnetoencephalography are new techniques of brain functional imaging which can provide the information of excitation of neurons by measure the changes of hemodynamics and electrophysiological data of local brain tissue. The purpose of this study was to study functional brain areas evoked by pure tones in healthy and sensorineural hearing loss subjects with these techniques and to compare the differences between the two groups. METHODS: Thirty healthy and 30 sensorineural hearing loss subjects were included in this study. In fMRI, block-design paradigm was used. During the active epoch the participants listened to 1000 Hz, sound pressure level 140 dB pure tones at duration 500 ms, interstimulus interval 1000 ms, which presented continuously via a magnetic resonance-compatible audio system. None stimulus was executed in control epoch. In magnetoencephalography study, every subject received stimuli of 1000 Hz tone bursts delivered to the bilateral ear at duration 8 ms, interstimulus intervals 1000 ms. Sound pressure level in healthy subjects was 30 dB; in sensorineural hearing loss subjects was 20 dB above everyone's hearing threshold respectively. All subjects were examined with 306-channel whole-scalp neuromagnetometer. RESULTS: In fMRI, all subjects showed significant activations in bilateral Heschl's gyri, anterior pole of planum temporale, planum temporale, precentral gyri, postcentral gyri, supramarginal gyri, superior temporal gyri, inferior frontal gyri, occipital lobes and cerebellums. The healthy subjects had more intensive activation in bilateral Heschl's gyri, anterior pole of planum temporale, inferior frontal gyri, left superior temporal gyri and right planum temporale than the hearing loss subjects. But in precentral gyri, postcentral gyri and occipital lobes, the activation is more intensive in the hearing loss subjects. In magnetoencephalography study, both in the hearing loss and the healthy subjects, the most evident audio evoked fields activated by pure tone were N100m, which located precisely on the Heschl's gyrus. Compared with the hearing loss subjects, N100m of the healthy subjects was stronger and had longer latencies in right hemisphere. CONCLUSIONS: Under proper pure tone stimulus the activation of auditory cortex can be elicited both in the healthy and the sensorineural hearing loss subjects. Either at objective equivalent stimuli or at subjectively perceived equivalent stimuli, the auditory responses were more intensive in healthy subjects than hearing loss subjects. The tone stimuli were processed in a network in human brain and there was an intrinsic relation between the auditory and visual cortex. Blood oxygen level dependent fMRI and magnetoencephalography could reinforce each other.

Acoustic Stimulation↗

PubMed2006

Different neurotropic pathogens elicit neurotoxic CCR9- or neurosupportive CXCR3-expressing microglia.

What mechanism that determines microglia accomplishing destructive or constructive role in CNS remains nebulous. We report here that intracranial priming and rechallenging with Toxoplasma gondii in mice elicit neurotoxic CCR9+ Irg1+ (immunoresponsive gene 1) microglia, which render resistance to apoptosis and produce a high level of TNF-alpha; priming and rechallenging with lymphocytic choriomeningitis virus elicit neurosupportive CXCR3+ Irg1- microglia, which are sensitive to apoptosis and produce a high level of IL-10 and TGF-beta. Administration of CCR9 and/or Irg1 small interfering RNA alters the frequency and functional profiles of neurotoxic CCR9+ Irg1+ and neurosupportive CXCR3+ Irg1- microglia in vivo. Moreover, by using a series of different neurotropic pathogens, including intracellular parasites, chronic virus, bacteria, toxic substances, and CNS injury to intracranially prime and subsequent rechallenge mice, the bi-directional elicitation of microglia has been confirmed as neurotoxic CCR9+ Irg1+ and neurosupportive CXCR3+ Irg1- cells in these mouse models. These data suggest that there exist two different types of microglia, providing with a novel insight into microglial involvement in neurodegenerative and neuroinflammatory pathogenesis such as Alzheimer's disease and AIDS dementia.

Animals↗

PubMed2006

[The animal research of recombinant adenovirus controlled by human telomerase reverse transcriptase promoter in the treatment of human prostate cancer].

OBJECTIVE: To approach the treatment efficiency of replication defective adenovirus carrying HSV-tk gene under control of the human telomerase reverse transcriptase (hTERT) promoter in a mouse xenografts model of prostate cancer. METHODS: It was erected that the model of human prostate cancer in BALB/C nude mouse followed by locally injecting Ad-hTERT-HSV-tk and peritoneal injection of GCV. The anti-tumor efficacy was evaluated by index of tumor volume, tumor weight, relative tumor curative, and tumor growth curve. Afterwards, the TUNEL and transmission electron microscope to overview apoptosis of tumor cells were used. Finally, immunohistochemistry for detecting PCNA of tumor cells were applied. RESULTS: Compared with the control group, all viruses treatment groups demonstrated tumor growth inhibition. Among 3 treatment groups, antitumoral effect of Ad-hTERT-HSV-tk/GCV was much stronger than other two groups (P < 0.05). Obvious necrosis and apoptosis was observed by TUNEL, and PCNA was detected by immunohistochemistry in tumor tissues in all viruses treatment group. CONCLUSIONS: Ad-hTERT-HSV-tk/GCV system is highly efficacious to inhabit the growth of human prostate cancer.

Adenoviridae↗

PubMed2006

Structural and functional insights into the regulation of Arabidopsis AGC VIIIa kinases.

The AGCVIIIa kinases of Arabidopsis are members of the eukaryotic PKA, PKG, and PKC group of regulatory kinases. One AGCVIIIa kinase, PINOID (PID), plays a fundamental role in the asymmetrical localization of membrane proteins during polar auxin transport. The remaining 16 AGCVIIIa genes have not been associated with single mutant phenotypes, suggesting that the corresponding kinases function redundantly. Consistent with this idea, we find that the genes encoding the Arabidopsis AGCVIIIa kinases have spatially distinct, but overlapping, expression domains. Here we show that the majority of Arabidopsis AGCVIIIa kinases are substrates for the 3-phosphoinositide-dependent kinase 1 (PDK1) and that trans-phosphorylation by PDK1 correlates with activation of substrate AGCVIIIa kinases. Mutational analysis of two conserved regulatory domains was used to demonstrate that sequences located outside of the C-terminal PDK1 interaction (PIF) domain and the activation loop are required for functional interactions between PDK1 and its substrates. A subset of GFP-tagged AGCVIIIa kinases expressed in Saccharomyces cerevisiae and tobacco BY-2 cells were preferentially localized to the cytoplasm (AGC1-7), nucleus (WAG1 and KIPK), and the cell periphery (PID). We present evidence that PID insertion domain sequences are sufficient to direct the observed peripheral localization. We find that PID specifically but non-selectively binds to phosphoinositides and phosphatidic acid, suggesting that PID might directly interact with the plasma membrane through protein-lipid interactions. The initial characterization of the AGCVIIIa kinases presented here provides a framework for elucidating the physiological roles of these kinases in planta.

3-Phosphoinositide-Dependent Protein Kinases↗

PubMed2006

Crystal structure of monomeric native antithrombin reveals a novel reactive center loop conformation.

The poor inhibitory activity of circulating antithrombin (AT) is critical to the formation of blood clots at sites of vascular damage. AT becomes an efficient inhibitor of the coagulation proteases only after binding to a specific heparin pentasaccharide, which alters the conformation of the reactive center loop (RCL). The molecular basis of this activation event lies at the heart of the regulation of hemostasis and accounts for the anticoagulant properties of the low molecular weight heparins. Although several structures of AT have been solved, the conformation of the RCL in native AT remains unknown because of the obligate crystal contact between the RCL of native AT and its latent counterpart. Here we report the crystallographic structure of a variant of AT in its monomeric native state. The RCL shifted approximately 20 A, and a salt bridge was observed between the P1 residue (Arg-393) and Glu-237. This contact explains the effect of mutations at the P1 position on the affinity of AT for heparin and also the properties of AT-Truro (E237K). The relevance of the observed conformation was verified through mutagenesis studies and by solving structures of the same variant in different crystal forms. We conclude that the poor inhibitory activity of the circulating form of AT is partially conferred by intramolecular contacts that restrain the RCL, orient the P1 residue away from attacking proteases, and additionally block the exosite utilized in protease recognition.

Amino Acid Sequence↗

PubMed2006

Agonistic monoclonal antibodies potentiate tumorigenic and invasive activities of splicing variant of the RON receptor tyrosine kinase.

Ligand-dependent or independent activation of the RON receptor tyrosine kinase is essential in transducing invasive signals leading to increased tumorigenic activities. In this study, we characterized two monoclonal antibodies (mAbs) specific to the extracellular domains of human RON and studied their agonistic effect on tumorigenic activities mediated by oncogenic variant RONDelta160. The mAb Zt/g4 and Zt/c1 are specific to human RON. They bind to RON with high affinities and recognized different epitopes on the RON extracellular domain. Because of their reactivity with native RON, Zt/g4 and Zt/c1 are useful in various applications such as immunoprecipitation, immunofluorescent analysis, and immunohistochemical staining. Functional studies revealed that Zt/g4 and Zt/c1 are capable of inducing RON phosphorylation which activates signaling proteins such as Erk1/2 and Akt. In NIH3T3 cells expressing RONDelta160, both mAbs significantly enhanced RONDelta160-mediated tumorigenic activities including cell proliferation, focus formation, and anchorage-independent growth. Cell shape changes with increased motile and invasive activities were also observed. Studies in vivo further demonstrated that Zt/g4 and Zt/c1 increase RONDelta160-mediated tumor growth in nude mice with a shortened time of onset and enlarged tumor volume. Thus, by recognizing specific epitopes on the RON extracellular domains, Zt/g4 and Zt/c1 have abilities to elicit a full array of RON-mediated responses. These mAbs will be useful in studying mechanisms underlying RON activation which lead to increased tumorigenic activities.

Animals↗

PubMed2006

Selective induction of necrotic cell death in cancer cells by beta-lapachone through activation of DNA damage response pathway.

Most efforts thus far have been devoted to develop apoptosis inducers for cancer treatment. However, apoptotic pathway deficiencies are a hallmark of cancer cells. We propose that one way to bypass defective apoptotic pathways in cancer cells is to induce necrotic cell death. Here we show that selective induction of necrotic cell death can be achieved by activation of the DNA damage response pathways. While beta-lapachone induces apoptosis through E2F1 checkpoint pathways, necrotic cell death can be selectively induced by beta-lapachone in a variety of cancer cells. We found that beta-lapachone, unlike DNA damaging chemotherapeutic agents, transiently activates PARP1, a main regulator of the DNA damage response pathway, both in vitro and in vivo. This occurs within minutes of exposure to beta-lapachone, resulting in selective necrotic cell death. Inhibition of PAR blocked beta-lapachone-induced necrosis. Furthermore, necrotic cell death induced by beta-lapachone was significantly reduced in PARP1 knockout cell lines. Our data suggest that selective necrotic cell death can be induced through activation of DNA damage response pathways, supporting the idea of selective necrotic cell death as a therapeutic strategy to eliminate cancer cells.

Animals↗

PubMed2006

Effect of Fructus Psoraleae on motility of gallbladder isolated smooth muscle strips from guinea pigs.

AIM: To observe the effect of Fructus Psoraleae on motility of isolated gallbladder muscle strips of guinea pigs and its mechanism. METHODS: Guinea pigs were hit to lose consciousness and the whole gallbladder was removed quickly. Two or three smooth muscle strips (8 mm x 3 mm) were cut along a longitudinal direction. The mucosa was gently removed. Every longitudinal muscle strip was suspended in a tissue chamber which was continuously perfused with 5 mL Krebs solution (37 degrees of C), pH 7.4, and aerated with 950 mL/L O2 and 50 mL/L CO2. The isometric response was recorded with an ink-writing recorder. After 2 h equilibration under 1 g-load, 50 microL Fructus Psoraleae (10, 20, 70, 200, 700, 1000 g/L) was added cumulatively into the tissue chamber in turn every 2 min to observe their effects on gallbladder muscle strips (cumulating final concentration of Fructus Psoraleae was 0.1, 0.3, 1.0, 3.0, 10.0, 20.0 g/L). The antagonists, including 4-DAMP, benzhydramine, hexamethonium, phentolamine, verapamil and idomethine were given 2 min before Fructus Psoraleae respectively to investigate the mechanisms involved. RESULTS: Fructus Psoraleae dose-dependently increased the resting tension (r = 0.992, P < 0.001), decreased the mean contractile amplitude (r = 0.970, P < 0.001) and meanwhile increased the contractile frequency of the gallbladder muscle strip in vitro (r = 0.965, P < 0.001). The exciting action of Fructus Psoraleae on the resting tension could be partially blocked by 4-DAMP (the resting tension decreased from 1.37 +/- 0.41 to 0.70 +/- 0.35, P < 0.001), benzhydramine (from 1.37 +/- 0.41 to 0.45 +/- 0.38, P < 0.001), hexamethonium (from 1.37 +/- 0.41 to 0.94 +/- 0.23, P < 0.05), phentolamine ( from 1.37 +/- 0.41 to 0.89 +/- 0.22, P < 0.01) and verapamil (from 1.37 +/- 0.41 to 0.94 +/- 0.26, P < 0.05). But the above antagonists had no significant effect on the action of Fructus Psoraleae-induced mean contractile amplitude (P > 0.05). Moreover, the increase of the contractile frequency due to Fructus Psoraleae was inhibited by 4-DAMP (decreased from 8.3 +/- 1.2 to 6.8 +/- 0.5, P < 0.01) and hexamethonium (from 8.3 +/- 1.2 to 7.0 +/- 0.9, P < 0.05). Idomethine had no significant effect on the Fructus Psoraleae-induced responses (P > 0.05). CONCLUSION: Fructus Psoraleae enhances the motility of isolated gallbladder muscle strips from guinea pigs, in a dose-dependent manner. The effect of Fructus Psoraleae is partly related to M3, N receptor, alpha receptor, H1 receptor, Ca2+ channel, but not related to prostaglandin.

Animals↗

PubMed2006

Human papillomavirus in the oral cavity of patients with and without renal transplantation.

This study investigates human papillomavirus (HPV) infection in the oral cavities of 88 Australian renal transplant recipients and 88 immunocompetent controls. Oral cavities were examined for lesions and brushings collected for HPV analysis by consensus PCR. No warts were identified; HPV DNA was detected in 18% of transplant versus 1% control samples (P<0.001). Cutaneous HPVs predominated. One patient had HPV16 in samples taken four years apart without evidence of associated lesions or malignancy. Transplant recipients were more likely than controls to have current cutaneous warts (P<0.001), fewer sexual partners (P=0.001), and to have never consumed alcohol (P=0.01). Among the transplant group, the risk of an HPV-positive sample was higher among older patients (P=0.05), and those with past cutaneous warts (P=0.04). This study extends previous surveys by encompassing overt and asymptomatic infection, a broad spectrum of cutaneous and genital HPVs, and by providing new data on risk factors for oral HPV infection.

Adult↗

PubMed2006

Host defence against C. albicans infections in IgH transgenic mice with V(H) derived from a natural anti-keratin antibody.

Fungal infections have been increasing and life-threatening in recent years, but host immune responses, especially the humoral immunity, to fungi have not been fully understood. In the present study, we report that natural antibodies from unimmunized mice bind to Candida albicans. We established a monoclonal natural antibody, 3B4, which recognized a surface antigen located at germ tubes of C. albicans. The 3B4 antibody protected mice from C. albicans-induced death in passive immunization, by mechanisms involving suppressing germ tube formation and modulating phagocytosis. Interestingly, 3B4 also bound to a self-antigen keratin. To further study the generation and anti-C. albicans activities of natural antibodies in vivo, we constructed a mu chain transgenic mouse (TgV(H)3B4) using the V(H) gene from 3B4. TgV(H)3B4 had elevated serum anti-keratin/C. albicans IgM, and were resistant to C. albicans infections. Analyses of B cell development showed that in TgV(H)3B4, B cells secreting the anti-keratin/C. albicans antibodies were enriched in the B1 B cell compartment. Our findings reveal an important role of keratin-reactive natural antibodies in anti-C. albicans immune responses, and suggest that keratin may function in selecting B cells into the B1 B cell compartment, where natural antibodies are made to fight fungal infections.

Animals↗

PubMed2006

An efficient implementation of the "cluster-in-molecule" approach for local electron correlation calculations.

An efficient implementation of the "cluster-in-molecule" (CIM) approach is presented for performing local electron correlation calculations in a basis of orthogonal occupied and virtual localized molecular orbitals (LMOs). The main idea of this approach is that significant excitation amplitudes can be approximately obtained by solving the coupled cluster (or Moller-Plesset perturbation theory) equations of a series of "clusters," each of which contains a subset of occupied and virtual LMOs. In the present implementation, we have proposed a simple approach for constructing virtual LMOs of clusters, and new ways of constructing clusters and extracting the correlation contributions from calculations on clusters, which are more efficient than those suggested in the original work. More importantly, linear scaling of computational time of the CIM approach is achieved by evaluating the transformed two-electron integrals over LMOs using simple truncation techniques in limited operations (independent of the molecular size). With typical thresholds, for a variety of molecules our test calculations demonstrate that more than 99% of the conventional MP2 or coupled cluster with doubles correlation energies can be recovered in the present CIM approach.

Journal Article↗

PubMed2006

Expression of K6W-ubiquitin inhibits proliferation of human lens epithelial cells.

PURPOSE: The ubiquitin-proteasome pathway plays an important role in controlling the cell cycle. The purpose of this study was to examine if expression of a dominant negative form of ubiquitin can inhibit the proliferation of lens epithelial cells. METHODS: Dominant negative K6W-ubiquitin was expressed in cultured human lens epithelial cells via an adenoviral vector. Cell proliferation was monitored by both cell counting and flow cytometry analysis. Protein levels of cell cycle regulators were assessed by western blotting. RESULTS: Expression of K6W-ubiquitin in lens epithelial cells prevented cell proliferation and specifically caused cell cycle delay/arrest in the G2/M phase. Consistent with the cell cycle delay/arrest in the G2/M phase, typical substrates of the ubiquitin-proteasome pathway and also M phase regulators such as cyclin A, cyclin B, and securin were stabilized by expression of K6W-ubiquitin. Cell cycle-dependent degradation of G1 phase regulators, such as the Cdk inhibitor p27KIP, was also inhibited by the expression of K6W-ubiquitin. CONCLUSIONS: These data demonstrate that the ubiquitin proteasome pathway plays an important role in regulating lens epithelial cell proliferation. Expression of dominant negative K6W-ubiquitin inhibits lens cell proliferation by inhibiting the degradation of cell cycle regulators.

Adenoviridae↗

PubMed2006

Interactions of daidzin with intramolecular G-quadruplex.

The potential interaction of daidzin, an ingredient of soy isoflavones, with human telomeric antiparallel G-quadruplex dAG(3)(T(2)AG(3))(3) was studied using ESI-MS, PAGE, CD and molecular simulation. Experimental studies indicated that daidzin molecules interacted with dAG(3)(T(2)AG(3))(3) and formed DNA-daidzin complex with the stoichiometric ratio of 1:1 and 1:2. The transition temperature of the G-quadruplex increased at higher ratio of daidzin to DNA. Under molecular crowding conditions the interactions between daidzin and the G-quadruplex become much stronger. Combining computational simulation and experimental results, it is demonstrated that the dAG(3)(T(2)AG(3))(3)/daidzin complex with a stoichiometric ratio of 1:1 is stabilized through the pi-pi conjugacy interactions and hydrogen bondings between daidzin and the bases of G-quadruplex. This work provides guidance not only on exploring the molecular anti-cancer mechanism of dietary isoflavones, but also searching small natural products as promising anticancer candidates that can inhibit telomerase activity.

Circular Dichroism↗

PubMed2006

Pro-urokinase-type plasminogen activator is a substrate for hepsin.

Hepsin, a type II transmembrane serine protease, is strongly up-regulated in prostate cancer. Hepsin overexpression in a mouse prostate cancer model resulted in tumor progression and metastasis, associated with basement membrane disorganization. We investigated whether hepsin enzymatic activity was linked to the basement membrane defects by examining its ability to initiate the plasminogen/plasmin proteolytic pathway. Because plasminogen is not processed by hepsin, we investigated the upstream activators, urokinase-type plasminogen activator (uPA) and tissue-type plasminogen activator. Enzymatic assays with a recombinant soluble form of hepsin demonstrated that hepsin did not cleave pro-tissue-type plasminogen activator but efficiently converted pro-uPA into high molecular weight uPA by cleavage at the Lys158-Ile159 (P1-P1') peptide bond. uPA generated by hepsin displayed enzymatic activity toward small synthetic and macromolecular substrates indistinguishable from uPA produced by plasmin. The catalytic efficiency of pro-uPA activation by hepsin (kcat/Km 4.8 x 10(5) m(-1) s(-1)) was similar to that of plasmin, which is considered the most potent pro-uPA activator and was about 6-fold higher than that of matriptase. Conversion of pro-uPA was also demonstrated with cell surface-expressed full-length hepsin. A stable hepsinoverexpressing LnCaP cell line converted pro-uPA into high molecular weight uPA at a rate of 6.6 +/- 1.9 nm uPA h(-1), which was about 3-fold higher than LnCaP cells expressing lower hepsin levels on their surface. In conclusion, the ability of hepsin to efficiently activate pro-uPA suggests that it may initiate plasmin-mediated proteolytic pathways at the tumor/stroma interface that lead to basement membrane disruption and tumor progression.

Animals↗

PubMed2006

Differentiation of hepatocytoid cell induced from whole-bone-marrow method isolated rat myeloid mesenchymal stem cells.

AIM: To explore the expansion and differentiation of hepatocytoid cell induced from myeloid mesenchymal stem cell (MSC) in vitro, in order to find suitable resource of hepatocytes for bioartificial liver or liver transplantation. METHODS: The rat myeloid MSC was isolated and divided into three groups which were cultured by Friedensteion method, and then were induced by culture fluid, culture fluid plus cholestatic serum and culture fluid plus hepatocyte growth factor (HGF), respectively. Hepatocytoid cell as well as expression of CK18 and AFP was observed by immunohistochemistry. RESULTS: After the induction for 21 d, hepatocytoid cell was observed, and its expression of CK18 and AFP was detected by immunohistochemistry in MSC cultured with cholestatic serum. Furthermore, on the 35th d, albumin mRNA was expressed in the cell, suggesting the inducing effect was similar to that by HGF. CONCLUSION: Rat myeloid MSC can differentiate into hepatocyte lineage under appropriate condition. This method is easy to operate.

Albumins↗

PubMed2006

Model-based analysis of tiling-arrays for ChIP-chip.

We propose a fast and powerful analysis algorithm, titled Model-based Analysis of Tiling-arrays (MAT), to reliably detect regions enriched by transcription factor chromatin immunoprecipitation (ChIP) on Affymetrix tiling arrays (ChIP-chip). MAT models the baseline probe behavior by considering probe sequence and copy number on each array. It standardizes the probe value through the probe model, eliminating the need for sample normalization. MAT uses an innovative function to score regions for ChIP enrichment, which allows robust P value and false discovery rate calculations. MAT can detect ChIP regions from a single ChIP sample, multiple ChIP samples, or multiple ChIP samples with controls with increasing accuracy. The single-array ChIP region detection feature minimizes the time and monetary costs for laboratories newly adopting ChIP-chip to test their protocols and antibodies and allows established ChIP-chip laboratories to identify samples with questionable quality that might contaminate their data. MAT is developed in open-source Python and is available at http://chip.dfci.harvard.edu/ approximately wli/MAT. The general framework presented here can be extended to other oligonucleotide microarrays and tiling array platforms.

Algorithms↗