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==Rui's gene list on 1000 BA8 neuronal single nuclei== ===Highlights=== # 12 groups in a hierarchical order by a bi-branching cluster strategy # 400 most differentially expressed genes were identified to separate 2 clusters in each round. ===Analysis description and links=== We collected 1064 single neuronal nucleus isolated from human brain Brodmann area 8. After a quality filter based on the difference between zero- and single-nucleus samples, 986 single nuclei were qualified to continue with clustering analysis. To identify neuornal cell types among these 986 samples, we measured similarity among expression profiles of all individual nuclei. The heat map reflecting correlation of each individual to all the others were used to guide for clustering. Correlations revealed two major nuclei population, which was differed significantly in genes expressed in GABAergic inhibitory neurons (GAD1/GAD2 etc.). The separation of these two clusters were further confirmed by K-means clustering and principle component analysis (PCA). We therefore performed a series of unbiased clustering approach that allows hierarchical bi-branching of samples based on gene expression profiles. By doing this, local rather than global gene expression pattern can be associated and subsets of nuclei can be identified based on genes with similar expression. All together, we divided 986 single-nucleus samples into 12 groups and identified 193 signature genes highly expressed in each defined group. [[File:12groups.jpg|500px]][[File:400genes_comp.jpg|500px]] ===Gene list=== * Criteria to choose full genes Starting from 986 single nuclei, we cluster these samples into two groups based on similarity of their gene expression. The most differentially expressed genes (p<0.05) causing such sample separation were identified, among which genes with a fold change at least 4 were chosen as "marker genes". Samples were kept clustering in such bi-branching strategy until 12 groups were identified. Altogether, 315 marker genes were identified responsible for each dividing. Genes are listed with log2(fold change) and ClusterID. For example, CBLN2's cluster ID is A1/2/3/4/5, which means it supports the first separation between A (A1/2/3/4/5) and B (B1/2/3/4/5/6/7) groups and up-regulated in A group. Among these 315 genes, they are 68 genes showing up in multiple separations (2-4). Some of the duplicate genes make perfect sense, such as BTBD11 showing up in B1/2/3/4/5/6/7, B1/2/3 and B1 cluster. However, some of them are not easily explain. Gene lists: [[media:genelist_Rui_upload_9.19.14.xlsx]] "HC_Gene" - list all genes based on separations, up-regulated level is presented as red; down-regulated level is in green. "duplicate_unique" - I separate 68 duplicated genes from 247 unique genes which only show up once. * Criteria to choose group specific genes Among 247 unique genes, I grab those identified at the very final separations. So there are 152 genes showing up-regulation in one of the 12 groups A1, A2, A3, A4, A5, B1, B2, B3, B4, B5, B6 and B7. Gene lists: [[media:genelist_Rui_upload_9.19.14.xlsx]] "12groupsGene" -
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