Classifying Medulloblastoma Subgroups Based on Small, Clinically Achievable Gene Sets

As treatment protocols for medulloblastoma (MB) are becoming subgroup-specific, means for reliably distinguishing between its subgroups are a timely need. Currently available methods include immunohistochemical stains, which are subjective and often inconclusive, and molecular techniques—e.g., NanoString, microarrays, or DNA methylation assays—which are time-consuming, expensive and not widely available. Quantitative PCR (qPCR) provides a good alternative for these methods, but the current NanoString panel which includes 22 genes is impractical for qPCR. Here, we applied machine-learning–based classifiers to extract reliable, concise gene sets for distinguishing between the four MB subgroups, and we compared the accuracy of these gene sets to that of the known NanoString 22-gene set. We validated our results using an independent microarray-based dataset of 92 samples of all four subgroups. In addition, we performed a qPCR validation on a cohort of 18 patients diagnosed with SHH, Group 3 and Group 4 MB. We found that the 22-gene set can be reduced to only six genes (IMPG2, NPR3, KHDRBS2, RBM24, WIF1, and EMX2) without compromising accuracy. The identified gene set is sufficiently small to make a qPCR-based MB subgroup classification easily accessible to clinicians, even in developing, poorly equipped countries

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原著和名: [記載なし]科名: ショウガ科 = Zingiberaceae採集地: タイ カオヤイ国立公園 (タイ国 カオヤイ国立公園)採集日: 1984/10/13採集者: 萩庭丈壽整理番号: JH015452国立科学博物館整理番号: TNS-VS-96545

Liriope spicata Lour.

原著和名: リウキウヤブラン コヤブラン科名: ユリ科 = Liliaceae採集地: 高知県 横倉山 (土佐 横倉山)採集日: 1965/8/8採集者: 萩庭丈壽整理番号: JH014910国立科学博物館整理番号: TNS-VS-96491

Additional file 6: Figure S6. of Elucidating tissue specific genes using the Benford distribution

The effect of different technical parameters on the Benford pattern as calculated based on cell line-derived gene expression data described as raw counts. If not mentioned otherwise read length was 100 bp and all reads were used in the analysis. Truncated reads (25 and 50 bp) and lower coverage (30, 50 and 80 % out of the total reads) appear in plot titles. The red line indicates the expected Benford distribution, symbol-marked lines are the distribution observed for three replicates. (PDF 17 kb

Lycopodium phlegmaria L.

原著和名: ヤウラクヒバ科名: ヒカゲノカズラ科 = Lycopodiaceae採集地: 鹿児島県 屋久島 屋久町 中瀬川中流 (大隅 屋久島 屋久町 中瀬川中流)採集日: 1976/12/22採集者: 古瀬 義整理番号: JH016031国立科学博物館整理番号: TNS-VS-96603

Fast Closure of N‑Terminal Long Loops but Slow Formation of β Strands Precedes the Folding Transition State of <i>Escherichia coli</i> Adenylate Kinase

The nature of the earliest steps of the initiation of the folding pathway of globular proteins is still controversial. To elucidate the role of early closure of long loop structures in the folding transition, we studied the folding kinetics of subdomain structures in <i>Escherichia coli</i> adenylate kinase (AK) using Förster type resonance excitation energy transfer (FRET)-based methods. The overall folding rate of the AK molecule and of several segments that form native β strands is 0.5 ± 0.3 s^–1, in sharp contrast to the 1000-fold faster closure of three long loop structures in the CORE domain. A FRET-based “double kinetics” analysis revealed complex transient changes in the initially closed N-terminal loop structure that then opens and closes again at the end of the folding pathway. The study of subdomain folding <i>in situ</i> suggests a hierarchic ordered folding mechanism, in which early and rapid cross-linking by hydrophobic loop closure provides structural stabilization at the initiation of the folding pathway