Abstract

AbstractToday’s data generation and analysis environment is changing rapidly as the lure of technologies provide new opportunities to laboratory scientists. From physicians seeking rapid translation to the bedside, to environmentalists seeking new paradigms to understand the biome - large scale data generation is everywhere. How do we overcome the challenges of curation, management, interpretation and sharing of these data in the new multidisciplinary environment? One key approach is to leverage the expertise inherent in existing systems - bringing together tools and paradigms that work in subfields, and making them work together for the consortium. We will discuss the stem cell discovery engine. The approach brings together leading experts in stem cell biology, molecular profiles from stem cell systems, and seeks to combine data from diverse platforms under the unifying theme of common biology. We explore the use of gene lists and canonical pathways as a supervisor - and present pathway fingerprinting as a molecular approach to a broader problem. We explore how the community seeks to interact with its data - under the glare of reality.

Highlights

  • Background built fromGEO corpus (120,000 chips)II Multi-study X-species data iPS ES Differentiating ES Adult differentiated Human Mouse Principal component (PC) 2Cross-species stem cell dataDifferentiation iPSES Differentiating ES Adult differentiated ‘Testis derived stem cells’ Conrad et al 2008‘Testis derived stem cells’ Conrad et al 2008 Human fibroblastsComparison with gene clusteringSpecies - specific effects dominatePluripotent pathway signature

  • Nature 2010, dispute Conrad claims based on gene level analysis we investigate the pluripotency of human adult germline0.0s0t1em cells (haGSCs) by using global gene- tures[2]

  • Broblast cells and in haGSCs and human fibroblast samples derived from diffeOrCeTn4t hTFCs) from them (Fig. 1a, b)k. haG2 SC3 s w4 er5e fo6un7d t8o b9e m10or1p1ho[12,13 14 15 16]

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Summary

Introduction

Background built fromGEO corpus (120,000 chips)II Multi-study X-species data iPS ES Differentiating ES Adult differentiated Human Mouse PC 2Cross-species stem cell dataDifferentiation iPSES Differentiating ES Adult differentiated ‘Testis derived stem cells’ Conrad et al 2008‘Testis derived stem cells’ Conrad et al 2008 Human fibroblastsComparison with gene clusteringSpecies - specific effects dominatePluripotent pathway signature. . stem cell researchers seek understanding of pluripotency . need to standardize understanding of cellular phenotypes that define stem cells and their progeny . Attention to standards, communication, data sharing Multi-study, single species; 5 different human ES/iPS gene expression studies combined to produce list of 20 differentially regulated genes in the transition from fibroblasts to iPS/ES cells hE

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