11月week1文献阅读：Global transcriptom

Global transcriptome analysis for identification of interactions between coding and noncoding RNAs during human erythroid differentiation.
全面转录分析验证人红系分化中编码与非编码RNA的相互作用

Abstract :
摘要
Methods:
方法
Fousing on the integration of the three RNA types, the writer compared the dynamics of coding genes,miRNA, and IncRNA expression profiles in erythropoiesis after taking advantage of high throughput sequencing technologies to obtain transcriptome data from cord blood hematopoietic stem cells and the following four erythroid differientiation stages and muture red blood cells.
集中于整合三种不同类型的RNA数据类型，作者再利用高通量技术获得造血干细胞，以及以后四个红系分化阶段二号成熟红细胞的转录数据后，比较了红系分化中编码RAN, miRNA, IncRNA的动态表达数据。

Results:
结果：
IncRNAs were promising cell marker candidates for erythroid differentiation.
IncRANs 有望成为红系分化的分子标志物。
Clustering analysis classified the differentially expressed genes into four subtypes that corresponded to dynamic changes during stemness maintenance, mid-differentiation, and maturation.
根据分化的动态变化性从干性的维持，到分化中期。到成熟期。对差异表达基因进行聚类分成四个子类。
Integrated analysis revealed that noncoding RNAs potentially participated in controlling blood cell maturation,and especially associated with heme metabolism and response to oxygen species and DNA damage.
整合分析揭示非编码RNAs潜在参与了成熟红细胞的形成，特别是和heme的代谢，携扬功能和DNA损伤有关。
These regulatory interactions were displayed in a comprehensive networks, thereby inferring correlations between RNAs and their associated funtions.

这些调控的相互作用被一个全面的调控网络呈现，有不同RNAs之间的联系和他们联系的功能作用。

Results:
Similar expression patterns of genes, miRNAs, and IncRNAs.
在gens, miRNA, IncRNAs中相似的表达模式。

Fig1

Fig1: Quantitative real-time PCR of several erythroid genes. A: Expression patterns of several erythroid genes validated using qRT-PCR B: Bar plots show the expression of patterns of eythroid genes during HSC development and in red blood cells.
定量实时PCR分析几个红系分化基因。
A: 用qRT-PCR验证 几个红系分化中基因的表达模式。
B: 这几个红系分化中基因的表达柱图，在HSC(造血干细胞)，分化和成熟细胞中的表达。
mRNA, miRNA, and IncRNA expression profiles.
mRNA,miRNA, IncRNA 表达图谱

Fig2A

A: Bar plotes showing numbers of expressed RNAs at various FPKM/RPKM levels.Most RNAs were expressed with FPKM lower than 30.A small number of mRNAs and miRNAs were expressed at a relatively high levelat above 100 FPKM.
柱图显示在不同 FPKM水平的表达数据分布， 大多数RNAs 表达的FPLKM低于 30， 少量的mRNAs 和 miRNA 表达在相对高水平（FPKM大于100）

fig2BCDE

B: Scatter plot of expressed IncRNAs in different eythroid differentiation stages.The y-axis represent the FPKM value of each IncRNA(colored dots). Few IncRNAs were expressed with FPKM > 30. C-D. Heatmatps of mRNA, miRNA and IncRNA expressions, respectively.
B: 不同红系分化时期的IncRNA 表达散点图， y轴代表 每个IncRNA的FPKM 的值。少量IncRNA 表达高于FPKM.
C-D: mRNA, miRNA, IncRNA 各自的表达热图。

K-means clustering of differentially expressed genes.
差异表达基因的K均值聚类

fig3

Genes that were highly expressed in differentitaion but signifcantly downregulated at muturation stage were classified under subtype 1.
在分化中高表达但是在成熟时期下调的基因被分为 子类1.
Genes that were higly expressed in HSC, but decreased at the following stages were classified under subtype 2.
在HSC(造血干细胞)中高表达，但是在随后分化阶段低表达的基因被分为 子类 2.
In subtype 3, gene expression gradually decreased during primary differentiation, but increased during maturation.
在子类 3 中，是风化阶段表达逐渐下调，但是在成熟阶段又高表达的基因。
The expression of genes altered more than once during differentiation were classified under subtype 4.
在分化中基因表达变化了不止一次的被分类为 子类4.
Transcription factors and hemoglobin, which were detected in distinct subtypes, are show on the right side of the figure.
转录和分化因子，在不同的子类中被检测到，显示在图右边。
Expressions of genes in signaling pathways were activated/inhibited during erythroid differentiation.
红系分化中，信号通路中基因表达被激活/抑制

fig4

A: Green nodes indicate genes that were decreased during maturation, whereas red nodes indicated genes that were increased.
绿色点表示基因下调在成熟中，红色代表增加。
Most of the genes in P53 pathway were inhibited. As TP53 was inhibited, the part of this pathway was supposed to be inative.
P53信号通路中大多数基因表达被抑制，随着TP53被抑制，此通路是被激活了。
B: Expression profiles of activated/inhibited genes in the p53 signaling pythways: 5 genes were upregulated during maturation, but 19 genes were observed downregulated during that peroid.
在p53信号通路中激活/抑制基因表达模式，在成熟期，5个基因被上调，19个基因被下调。

C: Expression profiles of chemokines in HSC. All know chemokines, except CCL13 and CCL18, were expressed in HSC and decreased during differentiation.
在HSC中趋化因子的表达模式。 所有已知的趋化因子，除了CCL13和CCL18 , 其它都在HSC表达并在分化过程中表达下调。
Correlation heatmap between miRNA and their target genes in subtype 3.
子类3中,miRNA 和靶基因的作用热图

fig5

Fifty miRNAs and 256 genes are shown in the left side of the figure. Subtypes 3 comprised 29 genes involved in 'metablism of heme' and reactive to oxygen species", among which 21 genes were possibly regulated by hsa-miR-532-3p, as highligted by the red box.
50个 miRNAs 和256 个基因 被显示在图右边， 子类3中包含的29个基因涉及heme的代谢和携氧激活，其中21个基因可能被hsa-miR-532-3p 调控，被红色方框标出。
Green color boxes represent significant negative correlation between miRNAs and target genes with Pearson correlation coeficient of <= -0.9 , p value <= 0.01(P values are not shown)
绿色方框代表miRNA和靶基因显著的负相关，Pearson 相关系数小于等于-0.9.P 值未显示。

Analysis of IncRNAs during erythroid differentiation.
红系分化中IncRNAs 的分析

fig6

A: Significant Pearson correlation coefiicient between 60 IncRNAs and coding genes with functions associated with "hemopoiesis and leucocyte activation" and "DNA repair".
显著的Pearson 相关性在60 IncRNAs 和 编码基因之间，这些编码基因和hemopoiesis以及 leucocyte 激活 以及 DNA 修复相关。

Postive correlations are colored red, whereas negative correlations are colored blue.正相关被标为红色，负相关被标为蓝色。

B: Expression patterns of RP11-326C3.2 and its downstream gene ATHL1 were validated using qPCR in the K562 cell line.
RP11-326C3.2和它的下游基因ATHL1被表达模式 被qPCP在K562细胞系中被验证。
C:Integrative Genomics Viewer expressed reads for RP11-326C3.2 and its downstream coding gene ATHL1 on chromosome 5.
整合 基因组视图 显示 RP11-326C3.2 和其下游编码基因 ATHL1在染色体5上的位置。

A comprehensive network illutrates the interations of coding genes, miRNAs, IncRNAs that participate in controlling red blood cell maturation.
全面的调控网络说明编码基因，miRNA, IncRN间的相互作用，起都参与了红细胞成熟的调控。

Fig7

Coding genes are marked with square nodes, whereas miRNAs and IncRNA are marked with "V" and round nodes,respectively.
编码基因用方向节点来标记，miRNA 用 V,IncRNA 用圆。
RANs that were upregulated during eythroid cell development are colored red, and downregulated RANs are colored green. RNAs downregulated during maturation, but not significant, were colored light green.

RNAs 在红系分化中上调的被标为红色，下调的被标为绿色，RNA,在成熟时下调，但是不明显的被标为浅绿色。