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MicroRNAs

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  • Page extent: 580 pages
  • Size: 253 x 177 mm
  • Weight: 1.22 kg

Library of Congress

  • Dewey number: 572.88
  • Dewey version: 22
  • LC Classification: QP623 .M53 2008
  • LC Subject headings:
    • RNA

Library of Congress Record

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 (ISBN-13: 9780521865982)

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  • Published December 2007

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MicroRNAs

Cambridge University Press
9780521865982 - MicroRNAs - From Basic Science to Disease Biology - Edited by Krishnarao Appasani
Index


Index

activated macrophages 513

acute lymphoblastic leukemia (ALL) 473

   adult leukemia 297

adapter protocol 78, 79

   oligo protocol 78

adenocarcinomas 265

adenoviruses 416

adipocyte differentiation 477

ageing 16

Agonaunte (AGO) gene family 8, 28, 309

   AGO1 367

   Ago2 86

   Ago3 503

      Ago protein isoforms 86, 98, 124

      Argonaute (AG) RNA binding 477

Arabidopsis thaliana 70, 71, 77, 79, 139, 145, 232, 287, 427, 434

   Arabidopsis miRNAs 79

   Arabidopsis Ago protein 498

Argonaute/Piwi (Ago/Piwi) family proteins 497

Agrobacterium tumedfaciens 504

Alzheimer’s disease 38, 125, 518

amplification 314, 502

   amplified real miRNA cDNAs 492

      AmpliTaq Gold DNA polymerase 270

Angelman syndrome 126

antagomirs 346

   antisense miRNAs 28

      antisense RNA probes 104

antiapoptotic factor 352

   anti-apoptotic protein Bc12 351, 330

anti-HIV drugs 38

   anti-targets 182, 423

   anti-viral vaccines 35

apical ectodermal ridge (AER) 62, 109

apoptosis 242, 275, 296, 301, 304, 313, 322, 324, 380, 489

arginine methylation 366

arrhythmias 517

ASE left (ASEL) and ASE right (ASER) 15, 50

astrocytes 352, 481

   astrocytic tumours 350

atopic dermatitis 513

AU rich elements (AREs) 225, 409

autism 125, 363

autosomal recessive 129

Auxin Response Factors (ARFs) 145

axonal transport 125


B-cell lymphoma 48, 302, 314, 329, 344, 472, 352

   B-cell differentiation 387, 470

   B-cell chronic lymphocytic leukemia 328, 380

      Bc12 (B-cell lymphoma 2) 313

      large cell lymphomas 332

   lymphoblastic leukemia (ALL) 372

      lymphocytes 373, 512

   lymphocytic leukemia cells 372, 472

      lymphoid malignancies 373

   lymphomagenesis 302, 330, 332

bacteriophage F1 DNA 24

Bantam 214, 296

basic helix–loop–helix transcription 301

BCL2 genes 378

   BCL2 protein expression 375

bead-based hybridization 46, 323

beta herpes viruses 410

beta-5 tubulin 222

bHLH family of transcription factors 142, 116, 402

BIC gene 472, 512

   Bic/miR-155 513

      Bic-deficient mice 513

bioinformatics 8, 70, 127, 146, 188

biomarkers 230

BLAST 72, 200, 454, 457

blastocyst 445

   blastocyst ICM 462

   blastoderm embryos 52

blood cell lineage 380

boosting 213

brain-derived neurotrophic factor (BDNF) 121

   brain miRNA expression 53

   brain morphogenesis 229

branched chain amino acids (BCAA) 129

breast cancer 298

   breast cancer-specific signature 316

   breast carcinoma 297

broncheoalveolar lavage fluids 513

Burkitt’s lymphoma (BL) 279, 298, 314, 332, 373, 407


Caenorhabditis elegans 7, 15, 18, 25, 30, 32, 42, 70, 72, 74, 79, 86, 116, 137, 159, 172, 178, 179, 180, 189, 199, 210, 211, 225, 238, 283, 295, 298, 299, 309, 310, 324, 331, 376, 392, 405, 427, 434, 497

   C. briggsae 179

   C. remanei 179

cancer 296, 310

   cancer diagnosis 297

   cancer-associated genomic regions 311

   cancerogenesis 312, 318

canonical translation initiation 92

Capase-9 330, 298

Cap-binding protein 87

cardiac 514

   cardiac conduction defect 31

   cardiac contractility 515

   cardiac hypertrophy 514

   cardiac muscle isoform 111

   cardiac transcription factor, Irx5 517

   cardiac-specific regulator 515

Castleman’s disease 407

CAT-1 338

CD10 372

CD19 372

   CD19 + B-lymphoid 470

CD40 513

cDNA library 71, 79

cell cycle regulation 489

   cell cycle delay 461

   cell death 65, 164, 269, 274

      cell diversity 514

   cell phenotype 314

      cell differentiation 489, 274, 296, 322, 398

      cell proliferation 48, 140, 242, 269, 274, 322

      cell specification 54

   cell type-specific expression 53

      cell type-specific genes 116

      cell type-specific transcription factors 117

cell-free translation systems 98

CGG trinucleotide repeats 364, 368

chain enhancer (Eμ-myc) 472

Chalamydomonas reinhardtii 519

chemotaxis 513

   chemoreceptor gene 15

chicken embryos 103

chromatin immunoprecipitation (ChIP) 301

   chromatin modification 242, 269

   chromatin remodeler 389, 507

   chromatoid body 508

chromosomal rearrangements 355

chromosomal translocation 328, 342

   chromosome 1 168

   chromosome 4 143

   chromosome 11 134

   chromosome 13 301

   chromosome 17 501

cis-regulatory elements 50, 51, 483

cloning of microRNA’s 117

c-Myc 298, 301, 329, 339, 342

   c-MYC protein 381

coefficient of variation (CV) 262

cognitive function 124

colorectal cancer 164, 297, 315, 352

combinatorial circuitry model 515

common lineage 519

component proteinase (Hc-Pro) 29

computational predictions 173, 158

   computational miRNA 158, 165

conditional Dicer allele 67

conserved recombination 373

contractility 514

control element-binding protein (CPEB) 95

co-suppression 137

CpG methylation 434

Cre-expression patterns 59

   Cre-expressing adenovirus 64

   Cre-mediated recombination 59, 515

   Cre protein 67, 325

CREB (camp Response Element Binding protein) 120

Cricket Paralysis Virus (CrPV) 92

cross-species comparison 176

CXCR4 88, 89

   CXCR4 miRNA 89, 90, 92

cytometry 46


Drosophila melanogaster 7, 12, 48, 53, 124, 131, 133, 143, 172, 174, 177, 178, 180, 201, 238, 249, 295, 324, 367, 377, 392, 402, 434, 471, 497, 502

D. pseudoobscura 52, 177, 178

   Drosophila embryogenesis 52, 95, 235

   Drosophila Piwi 498, 508

decarboxylation 130

deep sequencing methods 519

deletion or loss-of-heterozygosity 302

density gradients 86

development 164

   developmental fate 13

   developmental pathways 85

   developmental regulators 445

   developmental retardation 13

   developmental timing 13, 116, 117, 269

   developmental transitition 13

diabetes mellitus 296, 310, 518

diacylgycerol 381

Diana TarBasRNAhybrid 199

   DIANA-microT 178, 188, 189, 96

Dice-deficient progenitors 326

Dicer 25, 59, 66, 118, 124, 221, 269, 309, 367, 450, 492

   Dicer allele 63

   DICER LIKE (DCL) genes 139

   Dicer null blastocysts 461

   Dicer RNase III 477

      Dicer1 325

      Dicer1-/- 324

      Dicer2 461, 502

      Dicer-deficient ES cells 325

Dicer-deficient limbs 65, 66

   differentiation 53, 54, 229, 98, 312, 322, 164

disease biology 508

Distributed Annotation System (DAS) 169

Drsh-1 Drosha 8, 27, 46, 54, 59, 221, 269, 284, 409

DS-RNA binding motif 59

dynamic programming 201


E2f family of transcription factors 303

Early Embryonic microRNA cluster (EEmiRC) 479

early post-implantation embryos 462

   EEmiRC transcription unit 479

electrical conductance 514

embryonic cell biology 452

   embryogenesis 445, 499, 504

   embryonic development 10, 229

   embryonic lethality 59

   embryo to plasticity 116

embryonic fibroblast 492

   embryonic carcinoma (EC) 461, 479

embryonic stem (ES) cells 325, 445, 471, 476, 489

      embryonic stem cell differentiation 461, 479, 480, 484

      embryonic stem cell pluripotency 325

   embryonic germ (EG) cell lines 445

      endoderm-specific expression 109

      ESC-specific miRNAs 477

embryonic myosin 397, 398

endocrine disorders 31, 518

ensembl database 158

   ensembl coordinate system 162

epigenetic silencing 518

   epigenetic regulator 499

Epstein–Barr virus (EBV) 407

E-value 179, 208

evolutionary biology 13, 80

excision processing 35

exosomes 24

Exportin 5 7, 309

expressed sequence tag (EST) 339

extreme value distribution (EVD) 165


factor E2F1 330

fat metabolism 242, 324

female gamete generation 67, 183

fibrosis 515

fission yeast 518

flagella assembly 519

Flaviviridae 420

floral patterning 80

forelimbs 62, 65

forward genetic screens 10, 15

fragile chromosomal sites 225

Fragile X mental retardation 119, 124, 363, 366, 485

   Fragile X syndrome 164, 369


G:U wobble base pairing 177, 188, 207

gain-of-function 13, 16, 324, 330, 513

gamma herpes viruses 409, 410

GAPDH 247, 272, 287, 289, 290

gastrointestinal system 274

G-CSF receptor expression 471

gene therapy 35

gene expression programs 229

   gene expression signatures 47

   gene–expression profiles 333

gene nomenclature 158

   gene ontology 165, 195

genetic programming 212, 213

   genetic screens 146

   genome accessibility 29

      genome stability 295

genome-wide identification 459

   genomic organization 77

   genomic repeats 222

germ-line stem cells (GSC) 498, 505

glial cells 115

   glial tumorigenesis 351, 350

   glioblastoma 124, 354, 317, 353, 350, 355

   glioblatomas multiforme 350

global transcript profiling 142, 147

   global miRNA expression 297, 324

global repressor 116

glucose-induced insulin secretion 518

granulocytic differentiation 470, 471

Group II introns 30


He La cells 87, 89, 90, 182, 251

Helix–loop–helix (bHLH) 392

hematological malignancies 312

   hematopoiesis 229, 269, 310, 325, 326, 378, 380, 469

hepatocytes 346

   HepG2 cells 299, 344

   hepatocellular carcinoma 339

   herpes viruses 406

      Hepatitis C virus 347, 420

      herpes simplex virus-1 (HSV-1) 416

heterochromatin 29, 518

   heterochromatin silencing 119

   hetrochromatin protein 1(HP1) 498

heterochronic pathway 13

   heterochronic phenotypes 446

hidden Markov model (HMM) 180

hierarchical clustering 274

high-throughput genomics 238

   miRNA expression 46, 47, 243

   parallel pyro sequencing 518

HIV 38

   HIV-1 438

   HIV-1 p66 438

Hodgkin’s disease 298, 407, 513

   Hodgkin’s lymphoma (HD) 314, 472

Homo sapiens 172, 333, 454

homeobox gene regulation 15, 60, 229

homeostasis 513

hormone response 80

Hox genes 52, 60, 312

   Hox A, Hox B, Hox C, Hox D 275

      Hox-A11 400, 403

      Hoxb4 61

      Hoxb8 62, 63

Hsa-mir-663 159

hypertension 518

hypertrophy 514

hypodermis 13


imaginal disc 177

immune system 30, 310

   immune system development 296

immunoglobulin 373

   immunoglobulin heavy-chain enhancers 313

imprinting 489

in silico 190, 450, 482

   in silico methods 392, 479

in situ hybridization 33, 42, 48, 51, 53, 54, 61, 103, 104, 109, 234, 275, 514, 323

inflammation 514

inherited trait 129

initiation factor eIF6 98

innate immunity 514

insulin secretion 16, 229, 477

intergenic miRNAs 27

intronic microRNAs 22, 31, 37

invader let-7a assay 243, 246, 247

inverse-PCR 375

IRES-driven reporter mRNAs 96

ischemic heart disease 517, 518

islet-specific miRNA, miR-375 518


Karposi’s sarcoma-associated herpes virus (KSHV) 408, 409

kissing complex 365, 367

knock-out animals 512

KNOXI transcription factor 145

K-Ras mutant 324


lacZ transgene 61

large delta protein 344

large T-antigen (T-Ag) 418

larval development 10, 13

laser induced fluorescence (LIF) 256

latency associated transcript (LAT) 416

Lax repressor 7

leaf morphologies 145

Let-7 microRNA 15, 13, 25, 32, 44, 48, 58, 86, 95, 116, 150, 172, 199, 210, 214, 296, 315, 331, 446

Let-7 family 299

   Let-7a 247, 263

      Let-7-a-2 precursor 316

   Let-7b 109, 176, 263

   Let-7c 28, 247, 263, 396

Let-60 299

leukaemia 164, 275

   leukaemia inhibitory factor (LIF) 377

   leukemogenesis 298

   leukocytes 513

   leukosis virus (ALV)-induced lymphomagenesis 298

life-span regulation 229

ligation 78

limb development 58, 65, 67, 326

Limk1 121, 125

Lin-4 13, 25, 15, 42, 44, 86, 137, 173, 199, 210, 211, 296, 298, 446

Lin-14 13, 10, 16, 42, 137, 173, 211, 295

Lin-28 10, 189

Lin-41 13, 10, 175

lipofectamine 2000 88

locked nucleic acid (LNA)-modified oligonucleotides 33, 47, 53, 103, 230, 231, 236, 238, 256, 291, 323

   LNA antago-mirs 234, 237

   LNA probed in situ hybridization 494

   LNA/RNA hybrids 259

long-term depression (LTD) 366

loss of function 326, 39, 324, 330, 398

   mutants 13, 16

   transgenic 35

Lsy-6 microRNA 117, 119

   Lsy-6::GFP fusion 50

lung airway remodeling 513

lung cancer 48, 316, 332

   lung epithelium 326

   lung morphogenesis 67


M. musculus 172

machine learning 192, 211

macrophage differentiation 383

maintenance of stemness 489

maize 77

malignant glioblastoma 298

   malignant gliomas 350

mammalian homologue of Dhh1p, RCK/p54 96

   mammalian miR-1 52

   mammalian ortholog 298

   mammalian RNA polymerase type II (Pol-II) 33

mantle cell lymphoma 297

MAPK-associated protein kinase 2(MK2) 409

Maple syrup urine disease (MSUD) 129

Markov models (HMMs) 459

massively parallel signature sequencing (MPSS) 79

mature miRNAs 103

Me31B 97

medulloblastoma 275, 276

MEF protein family 392

   MEF2 (Myocyte Enhancer Factor 2) 122

   MEF-2 transcription factors 393

megakaryocytopoiesis 315

messenger ribonucleoprotein (mRNP) 364

metabolism 54, 269

metaphase II 505

methylation 314

metoazoans 177

mGluR5 366

microarray 42, 48, 103, 120, 353, 387

   microarray expression screening 47

   microarray platforms 46

microRNA biology 181

   microRNA expression profiles 33, 124, 351

   microRNA identification 78

microRNA invader 243

   microRNA microarray chips 310

   microRNA precursor hairpin 222

   microRNA precursors 126, 222

      microRNA registry 158

      microRNA target genes 8, 173

      microRNA target “network” 183

   microRNAs (miRNAs) 58

      microRNA:mRNA duplex 178, 175

      microRNA/target site duplexes 173

      microRNAs target interaction 12

   Mili and Miwi2 499, 506

miR -196a 48

MIR/LINE2 genomic repeats 222

MIR/LINE2 repeats 225

miR-1 48, 54, 74, 105, 182, 249, 296, 397, 514

   miR-1-1 50

   miR1-2 50

miR-2 family 177, 182

   miR-2/6/11/13/308 296

   miR-2a-2/2a-1/2b-2 53

miR-4 80

miR-5 77

mir-6 74

miR-7 177

miR-9 118

mir-9 262

miR-9 518

miR-10 52, 61, 74

   miR-10a 61, 62

   miR-10b 61, 297

miR-13 80

   miR-13a 214

   miR-13b-1/13a/2c 53

miR-14 296

miR-15 80, 351

   miR-15a 297

miR-16 77, 262, 265

   miR-16-1 51, 297, 311, 472

   Mir-163 primer 287

miR-17 109, 299, 301, 303

miR-20b 111

miR-21 298

mir-22 263

mir-22 265

miR-23b/24/27b 276

mir-24 265

miR-29a/29b 276

   miR29b 133

      miR29b-2 134

miR-32 419

miR-39 77, 80

mir-48 13

mir-84 13

mir-100 265

miR-122 339, 420

   miR-122a 45

miR-124 110, 176, 182, 352

   miR-124a 118

miR-125s 376

   miR-125b 297, 298

   miR125b-1 376

miR-126 110, 263, 265

miR-128 352

miR-132-mediated 120

miR-133 121, 125, 397, 481, 514

   miR-134 knockout 125

miR-138 109

miR 140s

   miR-142 380

   mir-143 263

   mir-144 109

   mir-145 263

   miR-145 297

   mir-146 109

   miR-146a 514

   miR-146b 514

miR-155 332, 314, 472

miR159a 147, 148

miR164 146, 235

miR165/166 146, 149

miR167 235

mIR169a 159

miR-170s

   miR-171 233

   miR172 149

miR-181 396, 398

   miR-181a 266

mir-191 263

miR192 133, 134

mir-195 265

mir-196 63

   miR-196a 61, 62

      miR-196a -1 61

      miR-196a -2 61

   miR-196b 61

mir-205 263, 266

miR-208 515

miR-210 183

miR-221 355

miR-223 311, 315, 469, 470

mir-241 13

miR-273 15, 117

miR277 135

mir-290 – miR-295 396, 457, 479

miR-300 394

miR-301 481

miR319 145, 149

   miR319a 147

miR-369 453

miR-375 176

miR-430 296

mir-664 159

miRanda 166, 177

   miRBase database 85, 157, 169, 229

miRBase sequences 159, 160, 165, 167

   miRBase targets 164, 167, 168

   miRBase version 105

   miR-BHRF1-1 407

miRNAs 85, 199, 405, 489

   miRNome 317

      miRNome expression 310

      miRNP 94

   miRNP formation 92

      miRNP/RISC complex 85

   miRNA “sensor 48

      miRNA abnormality 297

      miRNA annotations 157

      miRNA arrays 237

      miRNA assay 252

   miRNA binding sites 158

miRNA biology 18, 187, 326

   miRNA biogenesis 42, 46, 54, 137, 322, 467

      miRNA cleavage 407

      miRNA cloning 44, 48

      miRNA cluster 344, 457

   miRNA pathways 367, 149, 273, 278

      miRNA precursors(pre-miRNA) 33, 37, 143

   miRNA processing 32, 139

      miRNA promoter fusions 50

   miRNA recognition elements (MREs) 188, 419

miRNA target site recognition 66, 67, 77, 93, 139, 149, 157, 188, 194, 210, 211, 214, 218, 242

miRNA transcripts 51, 110, 406

miRNA database 286

miRNA detection and quantitation 252

   miRNA expression 10, 42, 46, 54, 237, 274, 276, 297, 480, 481

miRNA function 10, 88, 102

miRNA gene identification 10, 192, 194

miRNA hairpin 43, 191, 160

miRNA loss of function 143

miRNA microarray 316, 243

miRNA mutant phenotype 50

miRNA ortholog sequences 110

miRscan 411

monocotyledon 71

   granulocyte differentiation 381

Monodelphis domestica 457

mouse ESCs(mESCs) 476

MovingTarget 179, 181

messenger RNA (mRNA)

   mRNA precursor 22

   base pairing 85

      mRNA decapping 96

   mRNA cleavage 8, 86

      mRNA decay 477

   mRNA degradation 66, 87

      mRNA depletion 210

   mRNA expression patterns 42

      mRNA profiles 324

   mRNA splicing 125

   mRNA stability 507

   mRNA translation 8, 31, 86, 125

mRNA translocation 29

multiple myeloma 297

multi-vulva phenotype 15

murine embryo fibroblasts (MEFs) 53, 325

murine herpesvirus-68(MHV-68) 409

muscle-specific genes 393

   differentiation pathway 392

   muscle creatine kinase (MCK) 392, 396

   proliferation 229

   regeneration 396

muscular dystrophy 31

MYC gene 311

   MYC transcription 382

   Myc-induced lymphomas 314

myoblast cell lines 393

   myoblast differentiation 402

   myoblast profliferation 514

myogenesis 516

   myocardium 517

   myocyte hypertrophy 514

   MyoD expression 393

   MyoD family 392

      myogenin 400

   myosin heavy chain (MHC) 392, 515

   myotonic dystrophy 31, 38

   myotro-phin(Mtpn) 402, 518


N. benthamilana 235

N. crassa 427

NAC gene family 146

Nanog 445, 476, 481

Nanos mRNA 95

nascent protein degradation 98

NCI-60 cancer 275

necrosis 397

negative response element (NRE) 433

neoplasia 274, 275, 310

   neoplastic astrocytes 350

   neoplastic transformation 111

neural activity 53

   neural fates 481

neural stem cells 484

   neural progenitor cells 481

   neural-specific expression 109

   neural stem cell (NSC) differentiation 485

   neural stem cell differentiation 481

neurogenesis 481

   neurodegenerative disorders 310

   neurological 296

   neurological diseases 124

   neuron development 118, 242, 269

   neuronal differentiation 127, 324, 480

   neuronal morphogenesis 120

   neuronal networks 115

neuronal phenotype 118, 127

NF-kappaB-dependent gene 514

   NFI-A and C/EBPa 389

   NFI-A tranlation 315

Nicotiana benthamiana 232

   NKX2.1, transcription factor 3 382

N-myc 342

non-coding BIC (B-cell integration cluster) RNA 298

non-coding RNA (ncRNA) 22, 476

   Non-messenger RNA (nmRNA) 22

non-functions polysomes 346

non-LTR-retrotransposons 30

normal erythropoiesis 314

Northern Blot 44, 48, 64, 74, 102, 120, 231, 310, 315, 410

Neuronal Restricted Silencing Factor 118

nuclear RNA (snRNA) 24


Oct-4 445, 476

Oligoastrocytoma III grade 357

oligonucleotide/oligosaccharide-binding (OB) 498

   oligonucleotides 298

O-methyl antisense (AS) 298

oncogenes 111, 295, 358

   oncogenic miRNAs 318

   oncortroviruses 446

oligo peptide transporter 147

optimal model 213

organogenesis 15, 515

   organ polarity 146

orthologous miRNAs 207

   orthologous targets 202

Oryza sativa 71

Oskar 97

   Oskar mRNA 95

O-tetradecanoylphorbol-13-acetate(TPA) 381

oyster 55, 66, 259


processing (P) bodies 87, 96, 118, 498, 508

P21 400

P51 436, 438

P53 330

P66 436

paediatric Burkitts’s lymphomas 352

pancreatic insulin secretion 296, 472

   pancreatic β-cells 518

papillary thyroid carcinoma 317

paralogs 60

   paralogous miRNAs 50

Parkinson’s disease 38, 125

Pash-1 (DGCR8) 8

pathology 42

Pax and Hox families 393

PAZ: PIWI domain family of proteins 446

   PAZ domain 59, 497, 498

PDR-like ABC transporter 77

peripheral glial area (P) 353

Petunia plant 24

PFV-1 replication 420

phage DNA 24

   phage T4-derived 24

phenotypic defects 140

phosphorylation 78

photoreceptor cell differentiation 53, 229

phylogenetic analysis 498

PicTar 179, 180, 181

pigment expression 24

ping-pong mechanism 504

piRNA biogenesis 505

   piRNA library 503

   piRNA precursor 503

   piRNA/rasiRNA levels 502

   piRNAs 494, 500

pituitary adenoma 303

Piwi-interacting RNAs (piRNAs) 497, 500, 501, 503

Piwi homologs, prg-1 and prg-2 499

Planarians 518

   Planarian-specific miRNAs 518

plant development 139

pluripotent stem cell lines 445, 479

poly-cistronic primary transcripts 274

polyribosomes 364, 367

   Poly (A) polymerase 78

   Poly(A) tail 95, 96, 97, 285

   Polyadenylation 222

polycistronic miRNAs 468

polymerase II transcripts 338

polymerases type II (Pol-II) 23, 31

polymorphism 328

   Polymorphic variants 277

polyoma virus 418

Populus trichocarpa 80

post-embryonic development 499

posterior iridescent 31

post-synaptic densities (PSDs) 120

   post-transcriptional 42, 86

post-transcriptional gene silencing (PTGS) 25, 432

   post-transcriptional regulation 405

   post-translational modification 366

   post-transcriptional negative regulator 70

PPD proteins 498

Prader–Willi Syndrome 126

precocious phenotype 13

   precursor B-cell 372

   precursor messenger RNA (pre-mRNA) 27

   precursor miRNA hairpins 249

   precursor miRNA (pre-miRNA) 31, 159, 467

predicting microRNAs 483

premature RNA transcript (pre-miRNA) 59

pre-miRNA transcript 414

   pre-miR-367 453

   pre-miRNA hairpin 44, 235, 459

   pre-miRNA stem-loops 452

   pre-miRNAs 7, 26

preservative speech and language 363

primary effusion lymphoma (PEL) 407

primary mediastinal B cell lymphoma (PMBL) 314

primary miRNA transcripts (pri-miRNAs) 31, 43, 338

primary RNA transcript (pri-miRNA) 59, 160, 309

   Pri-miR-142 processing 54

   Pri-miRNA processing 8

   Pri-miRNA stem-loop 160

   Pri-miRNAs 26

   Pri-miRNAs 51

primordial germ cells (PGC) 445, 498

pro-arrhythmic factor 517

probe-miRNA hetero-duplex 245

progenitor cell 372

   progenitor/stem cells 323

   proliferation ES cells 396

prognosis 328

pro-inflammatory cytokines 514

proliferation 296, 322

pro-lymphoid leukemia 380

promoter fusions 42

prostate cancer 297

protein kinase R (PKR) 417

protein synthesis 24, 35

protein-coding gene 77

p-value 165, 166, 205, 208


quantitative RT-PCR 311

quantitation of miRNA expression 264


random shuffling 190

RA-receptor (RAR) binding site 482

RAS family 299

   Ras 331

   Ras/let60 signaling 15

RdRp assay 430

real-time PCR 492, 494

   real-time PCR-based miRNA profiling assay 489

   real-time quantification 269

receiver operating characteristics (ROC) 213

recombination 64, 507

regeneration 518

regulated in papillary thyroid carcinoma (PTC) 299

regulatory RNAs 102

Renilla Luciferase (RL) 188

repeat-associated siRNAs (rasiRNA) 501

retinoic acid (RA) 60, 481

   retinoic acid receptor B2 62

   retinoic-acid receptor α (RARα) 470

   retinoic-acid (ATRA) 470

retrotransposon 77, 505

retroviruses 30

   retroviridae 418

   retrovirus PRV-1 423

Rett-syndrome (RTT) 125

reverse transcription 270, 283, 490

   RT Assay 432, 428

reverse-genetic 199

RGG box 364

ribonuclease III 309

ribonucleoprotein K homology domains (KH domains) 364

ribonucleoprotein particles (RNP) 120

ribosomal RNA 23

   Ribosomal RNA (rRNA) genes 272

   Ribosomal transfer RNA products 323

   Ribosome drop-off 98

rice genome project 70

RISC (RNA-included silencing complex) 7, 284, 367, 380, 417, 446, 309

   RISC-incorporated miRNA 199

R-luc activity 89

R-luc or F-luc reporter constructs 95

RNA binding proteins 184

RNA cleavage 427

   RNA efficacy predictions 211

   RNA hairpin structure 221

RNA helicase 59, 124

RNA hybridization 77, 201

RNA induced silencing complex (RISC) 28, 31, 277, 284, 469

RISC (RNA-included silencing complex)

RNA interference RNAi) 7, 25, 137, 277, 405, 446, 467

   RNAi mechanism 62

   RNAi pathway 48, 427

   RNAi-mediated knockdown 126

RNA ligation 323

RNA polymerase II 23, 43, 50, 467, 410

RNA processing 29

RNA secondary structure 201

RNA splicing 28, 35, 77

RNA transport and translation 124

RNA22 484

RNA-binding protein (RBP) 120, 123

RNA-degrading enzymes (RNAses) 25

RNA-dependent RNA polymerase 420

RNA-directed RNA polymerase (RdRP) 427

RNAhybrid 179, 200, 202, 207, 208, 216

   RNAhybridDB 200

RNA-mediated cleavage 24

   RNA-mediated gene regulation 497

   RNA-mediated silencing pathway 137

RNA–protein complexes 85

RNaseIII family 58

   RNase H 398, 498

   RNAse III Drosha 27, 468

   RNase III enzyme Dicer 7, 28, 59

Rnase protection assays 242

root mean square deviation (RMSD) 450

RSS-like sequences 375

RT-PCR (real time RT-PCR) 270, 255, 242, 290, 384


S. pombe 446

Sanger Centre database 278, 289

scan RNAs 518

scarecrow-like transcription factor 77

Scmidtea mediterranea 518

seam cells 13

secondary reaction template (SRT) 243

seed 173

   seed region 199

   seed-free analysis 205

self-renewal 380

sensitive predictions 213

sensor strategy 48

separating hyper place 192

sequence repository 158

Sertoli cells 499

Sherman Paradox 364

short endogenous RNAs 229

short hairpin RNA 417

short interfering RNAs(siRNAs) 7, 24, 25, 72, 80, 137, 323, 432

siCXCR4 93

signal sequence (RSS) 373

Simian virus 40 418

single base pair mismatches 323

single molecule detection (SMD) platform 256, 257

single-stranded RNA (ssRNA) 242, 427

skeletal muscle-enriched, miR-133 393

small cell lung cancer 329

small modulatory RNA (smRNA) 23

small motor neuron protein 124

small non-messenger RNA 22

   small nuclear ribonucleoproteins (snRNP) 24

      small nucleolar RNA (snoRNAs) 23, 273, 278

   small regulatory RNA 22, 23

      small temporal (st) RNAs 25

Smith–Waterman type 177

social anxiety 363

solid tumors 318

somatic myotome 109

Sonic hedgehog 62

Sox2 476, 481

spatial information 10

Specific predictions 213

spermiogenesis 504

   spermatocytes 508

   spermatogenesis-related genes 498

spinal muscular atrophy 124

spliceosomal RNA 24

squamous cell carcinoma 265, 316

star sequence 159

statistical significance 202

stem cell fates 324

   Stem–loop finder (SLF) 410

   Stem–loop precursor 80

   stem–loop precursors 10

   Stem–loop printer 47

   Stem–loop RT primer 271, 489

   Stem–loop sequences 160

   Stem–loop sequences 406

support vector machines 192

support vector machines (SVMs) 191

SV40 3′-UTR 48

   SV40 associated small RNA (SAS) 418

   SV40 miRNAs 421

   SV40T antigen 421

synapse 127

   synaptic development 120

      synaptic development and plasticity 123, 124, 366

synaptic stimulation 121

synaptogenesis 122

synthetic intron (SpRNAi) consisting 33


T cell co-stimulation 513

T helper 2 (Th2) differentiation 513

T4 DNA ligase 79

   T4 RNA ligase 46, 448

tactile defensiveness 363

TaqMan miRNA assay 243, 269, 271, 272, 277, 276, 278

TaqMan probe-based real-time PCR 270, 490

TarBase 190, 194, 195

Target cleavage 174

Target predication algorithms 173, 175, 295

   Target prediction 8, 207, 211

   Target prediction method 181

   Target prediction programs 190

   Target recognition 175, 212

TargetBoost 215, 217

TargetScan 66, 178

TAT motif 460

   TAT-box 460

Tat-responsive-region (TAR)-binding protein(TRBP) 433

T-cell receptor (TCR) 373

   T-cell development 325

   TCP transcription factors 142

telomerase 23

temporal expression 10

termed miRNp or RISC 85

Tet-On or Tet-Off system 39

Tetrahymena thermophila 446, 518

Tetrahymena Piwi(Twi1P) 507

Tetraodon fugu 454

therapeutic intervention 54

thermodynamic binding stability 166, 211, 216

thyroid hormone receptor associated protein 1 515

tibialis anterior (TA) 396

timing of development 13

tiny non-coding RNA (tncRNA) 23

tissue-specific expression patterns 296

   tissue-specific pattern 310

   tissue-specificity 45

Toll-like receptors 513

TPA-induced differentiation 381, 383

training set 214

transamination reactions 129

transcript cleavage 148

transcriptional regulation 7

   transcriptional repression 506

   transcriptional silencing 446, 450

      transcriptome 85

transcription factor binding sites 50, 445

   transcription factor DAF-16 16

   transcription factor die-1 15

   transcription factor MAFB 315

   transcription factors NFI-A and C/EBPα 315

   transcription factors Oct4 481

transfer RNA (tRNA) 23

transgene quelling 25

transgenic animal models 38

   transgenic mouse 302

   transgenic plants 147

transient assay 139

translation 23

   translational efficiency 485

   translation control 225

   translation initiation 94

   translation repression 86, 95, 269

   translation silencing 485

   translational machinery 507

   translational regulation 498

   translational suppression 365

translational medicine 517

translocations 314, 343

transposable elements 30, 222

   transposon activity 30

   transposon silencing 505

trilogy 20, 257

tRNA-like transcripts 409

trophoblasitc stem (TS) cells 445

   trophoblast 445, 446

tumorigenesis 47, 295

   tumor profiling 47

   tumor growth arrest 313

   tumor progression 351

tumor suppressors 295, 358

   tumor suppressor genes (TSG) 327

   tumor suppressor genes map 311

tumor-specific miRNA signature 317

tumor-suppressor function 318

two-component strategy 49

two-dimensional gel electrophoresis 383

type Z diabetes 518


U6 RNA kits 247

UL36-1 414

ungapped alignment 212

universal RT-primer 283

uracil DNA glycosylase 415

uRT specific primers 289

3′untranslated region (3′-UTR) 8, 27, 42, 70, 102, 137, 139, 164, 166, 173, 175, 176, 182, 184, 204, 207, 214, 222, 225, 295, 317, 351, 364, 387, 484


V (D)J recombination 373, 374, 376, 378

valvular disease 518

vascular development 80

vertebrate development 477

vertebrate limb 58

viral DNA polymerase 407

   viral DNA replication 411, 416

viral infection 38, 164

   viral lifecycle 406

viral miRNAs 405

visuospatial cognition 125

vitro transcription 89

vulva 15


Watson–Crick base pairing 173, 199, 204, 230, 247

weighted sequence motifs 215

Williams Syndrome (WS) 125



X chromosome 29

   X-chromosome inactivation 31, 446

X mental retardation syndrome 38

Xenopus oocytes 24, 95

X-linked condition 31


zebrafish 38

   brain development 296

   Piwi (Ziwi) 505

   Zwill as Piwi-like genes 497

zeta-probe GT membranes 72

zinc finger transcription factor 15

zone of polarizing activity (ZPA) 62, 66


© Cambridge University Press


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