Assessing quality and normalization of microarrays: case studies using neurological genomic data.

Abstract:

BACKGROUND:Genomic analysis using microarray tools has the potential benefit of enhancing our understanding of neurological diseases. The analysis of these data is complex due to the large amount of data generated. Many tools have been developed to assist with this, but standard methods of analysis of these tools have not been established. OBJECTIVE:This study analyzed the sensitivity and specificity of different analytical methods for gene identification and presents a standardized approach. METHODS:Affymetrix HG-U133 plus 2.0 microarray datasets from two neurological diseases - chronic migraine and new-onset epilepsy - were used as source data and methods of analysis for normalization of data and identification of gene changes were compared. Housekeeping genes were used to identify non-specific changes and gender related genes were used to identify specific changes. RESULTS:Initial normalization of data revealed that 5-10% of the microarray were potential outliers due to technical errors. Two separate methods of analysis (dChip and Bioconductor) identified the same microarray chips as outliers. For specificity and sensitivity testing, performing a per-gene normalization was found to be inferior to standard preprocessing procedures using robust multichip average analysis. CONCLUSIONS:Technical variation in microarray preprocessing may account for chip-to-chip and batch-to-batch variations and outliers need to be removed prior to analysis. Specificity and sensitivity of the final results are best achieved following this identification and removal with standard genomic analysis techniques. Future tools may benefit from the use of standard tools of measurement.

journal_name

Acta Neurol Scand

authors

Hershey AD,Burdine D,Liu C,Nick TG,Gilbert DL,Glauser TA

doi

10.1111/j.1600-0404.2007.00979.x

subject

Has Abstract

pub_date

2008-07-01 00:00:00

pages

29-41

issue

1

eissn

0001-6314

issn

1600-0404

pii

ANE979

journal_volume

118

pub_type

杂志文章
  • Blepharoclonus and Arnold-Chiari malformation.

    abstract:OBJECTIVE:Blepharoclonus (BLC) denotes a large amplitude, involuntary tremors of the orbicularis oculi muscles, observed during gentle closure of the eyelids. BLC may follow major head trauma. Four patients with Arnold-Chiari malformation (ACM) and BLC are described. MATERIALS AND METHODS:The first patient had facial ...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1034/j.1600-0404.2001.104002113.x

    authors: Jacome DE

    更新日期:2001-08-01 00:00:00

  • Neuropsychological tests are useful for predicting comorbidities of idiopathic normal pressure hydrocephalus.

    abstract:OBJECTIVES:Comorbidities of idiopathic normal pressure hydrocephalus (iNPH), such as Alzheimer's disease (AD) and Parkinson's spectrum (PS) disorder, can affect the long-term prognosis of cerebrospinal fluid (CSF) shunting. Therefore, it is important to be able to predict comorbidities in the early stage of the disease...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/ane.13306

    authors: Kamohara C,Nakajima M,Kawamura K,Akiba C,Ogino I,Xu H,Karagiozov K,Arai H,Miyajima M

    更新日期:2020-12-01 00:00:00

  • Valproate in children with newly diagnosed idiopathic generalized epilepsy.

    abstract:OBJECTIVES:Sparse information on dose-response characteristics for initial antiepileptic drug monotherapy in children with idiopathic generalized epilepsy (IGE) is available. The aim of this study is to characterize the therapeutic dose of valproate in children with newly diagnosed IGE. MATERIALS AND METHODS:Effect of...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.2009.01308.x

    authors: Holland KD,Monahan S,Morita D,Vartzelis G,Glauser TA

    更新日期:2010-03-01 00:00:00

  • Cognition in non-demented Parkinson's disease vs essential tremor: A population-based study.

    abstract:OBJECTIVES:Patients with Parkinson's disease (PD) and essential tremor (ET) have a higher risk of cognitive impairment than age-matched controls. Only a few small studies (11-18 subjects per group) have directly compared the cognitive profile of these conditions. Our aim was to compare the cognitive profile of patients...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/ane.12752

    authors: Sánchez-Ferro Á,Benito-León J,Louis ED,Contador I,Hernández-Gallego J,Puertas-Martín V,Bermejo-Pareja F

    更新日期:2017-11-01 00:00:00

  • A further study on the prevalence of multiple sclerosis in Sicily: Caltanissetta city.

    abstract::The prevalence of probable multiple sclerosis (MS) in Caltanissetta city, Sicily, is at least 51 per 100,000. If possible multiple sclerosis patients are included, it is 54 per 100,000. This value is similar to that found in other cities in Sicily: Enna, Monreale and Agrigento. The high prevalence of multiple sclerosi...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1986.tb03243.x

    authors: Savettieri G,Elian M,Giordano D,Grimaldi G,Ventura A,Dean G

    更新日期:1986-01-01 00:00:00

  • Pre-traumatic conditions can influence cortisol levels before and after a brain injury.

    abstract:OBJECTIVE:Satisfactory anabolic reactions, including the activation of the hypothalamic-pituitary-adrenal (HPA) axis, are essential following severe traumatic brain injury (TBI) and aneurysmal subarachnoid hemorrhage (SAH). Many factors may influence this activation. This study aimed to investigate whether individuals ...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/ane.13212

    authors: Sörbo A,Eiving I,Theodorsson E,Rydenhag B,Jonsdottir IH

    更新日期:2020-04-01 00:00:00

  • Experimental studies and controlled clinical testing of valproate and vigabatrin.

    abstract::Gamma-aminobutyric acid (GABA) is the most important inhibitory transmitter, quantitatively, in the CNS. Evidence exists that decreased GABAergic neurotransmission may play a role in some forms of epilepsy. Consequently, manipulating the GABA system may be a therapeutic possibility in the treatment of this disease. In...

    journal_title:Acta neurologica Scandinavica

    pub_type: 临床试验,杂志文章,评审

    doi:10.1111/j.1600-0404.1988.tb03655.x

    authors: Gram L

    更新日期:1988-10-01 00:00:00

  • Ex vivo release of eicosanoids after aneurysmal subarachnoid hemorrhage: a preliminary experience in humans.

    abstract::Authors addressed the question whether the byosynthesis and the release of specific eicosanoids may occur in human brain cortex, and if the qualitative pattern of arachidonic acid metabolism is similar to that observed in experimental SAH. Human brain samples from 18 patients operated on for anterior communicating art...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1992.tb05063.x

    authors: Gaetani P,Marzatico F,Rodriguez y Baena R

    更新日期:1992-08-01 00:00:00

  • B cell activation in multiple sclerosis.

    abstract::A microtechnique was established for the study of the limited numbers of cells available in CSF. The method allowed for the determination of the number of immunoglobulin-secreting cells (IgSC) as well as the quantitation of immunoglobulin or specific antibody secreted into the culture medium. Dose-response curves and ...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1986.tb07866.x

    authors: Sandberg M,Levinson AI,Zweiman B,Lisak RP

    更新日期:1986-12-01 00:00:00

  • Bell's palsy: a manifestation of prediabetes?

    abstract:BACKGROUND:Idiopathic peripheral facial nerve palsy or Bell's palsy (BP) is the most common cause of facial nerve palsy. OBJECTIVE:To evaluate the role of glucose metabolism abnormalities in BP. METHODS:We identified 148 patients with unilateral BP and 128 control subjects. In all we evaluated glucose level at fastin...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.2010.01365.x

    authors: Bosco D,Plastino M,Bosco F,Consoli A,Labate A,Pirritano D,Consoli D,Fava A

    更新日期:2011-01-01 00:00:00

  • Incidence of the urological tumours in patients suffering from multiple sclerosis.

    abstract:OBJECTIVES:The goal of this study was to evaluate the incidence of urological malignancies in MS patients using active screening. MATERIAL AND METHODS:A total of 495 MS patients (141 men, 354 women, age of 42±13.4) were included in the study. The duration of disease was 12.3±11 years, and the EDSS score was 4.3 (±2.5)...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/ane.12264

    authors: Krhut J,Hradilek P,Nemec D,Tvrdik J,Zapletalova O,Zvara P

    更新日期:2014-09-01 00:00:00

  • N20 and P40 somatosensory evoked potentials: thalamic lesions and subcortical origin.

    abstract::Three patients with well-defined clinical and radiographic lesions have been studied with somatosensory evoked potentials (SSEPs). The data indicate that the primary scalp potentials from stimulation of both the arm and leg (N20 and P40) can be lost with thalamic lesions and would be consistent with these potentials b...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1985.tb03162.x

    authors: Fisher MA,Perlik SJ

    更新日期:1985-01-01 00:00:00

  • Serum of concentrations of immunoglobulins in patients with epilepsy treated with carbamazepine.

    abstract::The concentrations of IgA, IgG and IgM were determined in sera of 16 patients, all of whom had partial epilepsy and had received CBZ as the only drug since the beginning of therapy. Fifty-three healthy subjects served as controls. Serum concentrations of IgA and IgG were significantly higher in patients than in contro...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1980.tb01491.x

    authors: Strandjord RE,Johannessen SI,Aarli JA

    更新日期:1980-04-01 00:00:00

  • The evidence for switching dibenzazepines in people with epilepsy.

    abstract::The dibenzazepines particularly carbamazepine are associated with known adverse effects (AEs) and drug to drug interactions. Eslicarbazepine acetate (ESL) is structurally distinct from other members of the dibenzazepine family and has the advantage of once daily dosing. Observational and trial data report successful s...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章,评审

    doi:10.1111/ane.13248

    authors: Watkins L,O'Dwyer M,Oak K,Lawthom C,Maguire M,Thomas R,Shankar R

    更新日期:2020-08-01 00:00:00

  • Valproate-associated foetal malformations-Rates of occurrence, risks in attempted avoidance.

    abstract:OBJECTIVES:To gain insight into the main advantages and disadvantages that might result from valproate being unavailable for women who intend to become pregnant. MATERIALS AND METHODS:Analysis of data from the Australian Pregnancy Register concerning pregnancies exposed to valproate (N = 501) and pregnancies where pre...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/ane.13005

    authors: Vajda FJE,O'Brien TJ,Graham JE,Hitchcock AA,Lander CM,Eadie MJ

    更新日期:2019-01-01 00:00:00

  • Long-term epidemiology of multiple sclerosis in the Northern Seville District.

    abstract:OBJECTIVES:Comprehensive epidemiologic data for multiple sclerosis (MS) in Spain are limited. The aim of this study was to collect epidemiologic data on MS in the Northern Seville District of Spain. MATERIALS AND METHODS:This longitudinal study identified possible MS cases every year from nine centres between 1 Januar...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章,多中心研究

    doi:10.1111/ane.12363

    authors: Izquierdo G,Venegas A,Sanabria C,Navarro G

    更新日期:2015-08-01 00:00:00

  • Hemispheric differences in the duration of focal onset seizures.

    abstract:OBJECTIVE:To assess hemispheric differences in the duration of focal onset seizures and its association with clinical and demographic factors. METHODS:A retrospective analysis was performed on adult patients with drug-resistant unifocal epilepsy, who underwent intracranial EEG recording between 01/2006 and 06/2016. Se...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/ane.13356

    authors: Seethaler M,Lauseker M,Ernst K,Rémi J,Vollmar C,Noachtar S,Kaufmann E

    更新日期:2020-10-04 00:00:00

  • Arachnoid cysts of the middle cranial fossa: a clinical, radiological and follow-up study.

    abstract::Twenty-seven patients with CT-scan-diagnosed arachnoid cysts in the middle cranial fossa were studied. Five (18%) presented with progressive symptoms related to raised intracranial pressure which had developed after minor trauma and secondary bleeding, 12 (44%) presented with non-progressive symptoms, and 10 (37%) exh...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1990.tb01595.x

    authors: Passero S,Filosomi G,Cioni R,Venturi C,Volpini B

    更新日期:1990-08-01 00:00:00

  • Perampanel Study 207: long-term open-label evaluation in patients with epilepsy.

    abstract:OBJECTIVES:Evaluate interim long-term tolerability, safety and efficacy of adjunctive perampanel, a novel α-amino-3-hydroxy-5-methyl-5-isoxazolepropionic acid (AMPA)-receptor antagonist, in patients with refractory partial-onset seizures. MATERIALS AND METHODS:Study 207, an open-label extension (OLE) study (ClinicalTr...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章,多中心研究,随机对照试验

    doi:10.1111/ane.12001

    authors: Rektor I,Krauss GL,Bar M,Biton V,Klapper JA,Vaiciene-Magistris N,Kuba R,Squillacote D,Gee M,Kumar D

    更新日期:2012-10-01 00:00:00

  • New subcortical components of the cerebral somatosensory evoked potential in man.

    abstract::Two new components of the human SEP upon stimulation of the contralateral median nerve at the wrist have been identified. Such components have been called N16 and N17, according to their polarity and latency. N16 and N17, as well as the N14-P15 complex, are generated by separate subcortical dipoles. Particularly, they...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1978.tb02896.x

    authors: Abbruzzese M,Favale E,Leandri M,Ratto S

    更新日期:1978-12-01 00:00:00

  • Influence of carbamazepine on serum thyroxine and triiodothyronine in patients with epilepsy.

    abstract::Hypothyroidism induced by anti-epileptic drug treatment gave rise to thyroid function test studies in patients treated with carbamazepine (CBZ) only. In 42 patients on long-term CBZ treatment thyroxine (T4), free T4-index (FT4I), and triiodothyronine (T3) concentrations in serum were significantly lower than in contro...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1981.tb00754.x

    authors: Strandjord RE,Aanderud S,Myking OL,Johannessen SI

    更新日期:1981-02-01 00:00:00

  • Effect of long-term L-threo-3,4-dihydroxyphenylserine administration on alpha 2-adrenergic receptors in platelet membranes in neurologic disorders.

    abstract::The effects of L-threo-3,4-dihydroxyphenylserine (L-threo-DOPS), an unnatural norepinephrine precursor, on alpha 2-adrenergic receptors in platelet membranes were investigated in a patient with familial amyloidotic polyneuropathy, two patients with multiple system atrophy, and two patients with Parkinson's disease. Ea...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1991.tb04901.x

    authors: Azuma T,Suzuki T,Sakoda S,Mizuno R,Tsujino S,Kobayashi T,Kishimoto S,Hiraga T,Matsubara T,Yoshida S

    更新日期:1991-07-01 00:00:00

  • Autosomal recessive paraparesis with amyotrophy of the hands and feet.

    abstract::We present 2 sibs with autosomal recessive spastic paraparesis and severe amyotrophy of the distal limb muscles. Elaborate neurophysiologic studies disclosed slight to moderate slowing of motor conduction, moderate to severe reduction of motor action potentials, denervation potentials, and increased distal motor laten...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1993.tb04133.x

    authors: Bruyn RP,Scheltens P,Lycklama à Nijeholt J,de Jong JM

    更新日期:1993-06-01 00:00:00

  • Temporal arteritis: a decision-analytic approach to temporal artery biopsy.

    abstract::The clinical indications for temporal artery biopsy were explored using clinical decision analysis. The analysis indicated that biopsy is most useful in patients with a high likelihood of steroid side effects. It is nearly always useful when the pre-biopsy likelihood of temporal arteritis is low, but loses its value w...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1988.tb03627.x

    authors: Nadeau SE

    更新日期:1988-08-01 00:00:00

  • Hereditary spastic paraplegia with neurogenic bladder disturbances and syndactylia.

    abstract::The present paper reports a family settled in the northern part of Norway, with a hereditary neurological disorder consisting clinically of spastic paraplegia associated with neurogenic bladder disturbances and syndactylia. Nine out of 22 members in three generations exhibit these clinical features. The bladder distur...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1980.tb02993.x

    authors: Opjordsmoen S,Nyberg-Hansen R

    更新日期:1980-01-01 00:00:00

  • Muscular cramps: proposals for a new classification.

    abstract::Muscle cramps are involuntary, painful, sudden contractions of the skeletal muscles. They are present in normal subjects under certain conditions (during a strong voluntary contraction, sleep, sports, pregnancy) and in several pathologies such as myopathies, neuropathies, motoneuron diseases, metabolic disorders, hydr...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章,评审

    doi:10.1034/j.1600-0404.2003.01289.x

    authors: Parisi L,Pierelli F,Amabile G,Valente G,Calandriello E,Fattapposta F,Rossi P,Serrao M

    更新日期:2003-03-01 00:00:00

  • Combination total lymphoid irradiation and low-dose corticosteroid therapy for progressive multiple sclerosis.

    abstract::Total lymphoid irradiation (TLI) has been reported to delay deterioration in patients with progressive multiple sclerosis and other autoimmune disorders. METHODS--In an open trial, the effect of TLI combined with a one year course of low dose prednisone was compared to the effect of sham TLI and TLI only in a prior do...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1995.tb05838.x

    authors: Cook SD,Devereux C,Troiano R,Bansil S,Zito G,Sheffet A,Jotkowitz A,Rohowsky-Kochan C,Dowling PC

    更新日期:1995-01-01 00:00:00

  • Femoxetine - a new 5-HT uptake inhibitor - and propranolol in the prophylactic treatment of migraine.

    abstract::The prophylactic effect of a 5-HT uptake inhibitor, femoxetine, was compared with that of propranolol in a double-blind crossover study of 6-months duration. 29 patients commenced the experiment. 3 subjects withdrew because of side effects and 2 because the program was inconvenient for them. In the 24 patients who con...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1983.tb04836.x

    authors: Kangasniemi PJ,Nyrke T,Lang AH,Petersen E

    更新日期:1983-10-01 00:00:00

  • Examination of the SLITRK1 gene in Caucasian patients with Tourette syndrome.

    abstract:OBJECTIVE:To determine whether variants in the Slit and Trk-like 1 gene (SLITRK1) are present in American Caucasian population of patients with Tourette syndrome (TS). METHODS:We sequenced the 3'-untranslated region for var321 and the whole coding region in the SLITRK1 gene in 82 Caucasian patients with TS from North ...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.2006.00706.x

    authors: Deng H,Le WD,Xie WJ,Jankovic J

    更新日期:2006-12-01 00:00:00

  • Altered blood-brain-barrier function in Alzheimer's disease?

    abstract::Alzheimer's disease (AD) and vascular dementia (VD) are the two most common causes of dementia. As yet, no definitive biological antemortem marker has been established for differential diagnosis of AD or VD. In this study, proteins of cerebrospinal fluid (CSF) from AD, VD and control patients were analyzed by two-dime...

    journal_title:Acta neurologica Scandinavica

    pub_type: 杂志文章

    doi:10.1111/j.1600-0404.1994.tb01660.x

    authors: Mattila KM,Pirttilä T,Blennow K,Wallin A,Viitanen M,Frey H

    更新日期:1994-03-01 00:00:00