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Analysis Results

by Thomas Girke — last modified Jul 19, 2014 01:48 AM

(A) Sample Clustering

Sample Clustering

Fig 1. Sample Tree: Clustering of all cell samples (CEL files)
Download correlation matrix (method: Spearman).

(B) Gene Clustering





HC2

Fig2. Hierarchical Clustering with Heatmap


  • Download table for heatmap. Corresponding GO results for clusters.
  • Enrichment Summary with and without outliers (also in heatmap table):
AtHB8   119    833
CLV3p      7     32
FILp        11     50
GL2p        6     34
HMGp       6     63
KANp       9      45
L1p          3      37
LASp        3      17
S17Sp  271  1005
WUSp     11      55

OL Matrix Enrsichment Data
Intersect Map of Enrichment Gene Sets (intersect matrix)



OL Mean Expression (Row Scale)


OL Mean Expression (Col Scale)





fuzzy22new

Fig3 A. Fuzzy Clustering: K=22
Tabular results in above master table.
Corresponding GO results for clusters.


Motif Discovery for Fuzzy Clustering K=22




fuzzy15
Fig3 B. Fuzzy Clustering: K=15
Corresponding GO results for clusters.



fuzzy10
Fig3 C. Fuzzy Clustering: K=10
Corresponding GO results for clusters.



(C.1) DEG and Motif Analysis of HMGp, GL2p and L1p



threewayvenn

Enrichment of known motifs

Pattern TAAATGCA (Plant J. 26, 487-494): 9 matches in 130 L1p set, 51 matches in 1000 random promoters, enrichment p-value: 0.2068551

Pattern TAAATGTA (Plant J. 26, 487-494): 11 matches in 130 L1p set, 95 matches in 1000 random promoters, enrichment p-value: 0.7161801


Motif Discovery

Motif Searches in 1kb upstream of DEGs common in all 3 possible comparisons. GO term enrichment analysis for all three samples.


Ram's Final Motif Discovery (May 18, 2011)

HMGp_GL2p_WUSp_statsDF.xls

CLV3p_FILp_KANp_LASp_statsDF.xls

Ram's Final Agris Motif Finding (May 19, 2011)

agris_Ram_HMGp_GL2p_WUSp.xls
agris_Ram_CLV3p_FILp_KANp_LASp.xls




(C.2) Layers: DEG and Motif Analysis of HMGp, GL2p, L1p and WUSp


vennHMGp_GL2p_L1p_WUSp

GO Results for Enrichment Sets in heatTable

Motif Discovery

Motif Searches in 1kb upstream of DEGs.

Motif Finding


(C.3) Zones: DEG and Motif Analysis of CLV3p, LASp, and KANp


vennCLV3p_LASp_KANp

GO Results for Enrichment Sets in heatTable

Motif Discovery

Motif Searches in 1kb upstream of DEGs.


Motif Finding

Enrichment of Agris motifs

(D) Root-SAM Comparisons


Root SAM Venn


Venn Diagram of Root-SAM Present Genes (gene list)

Root Sam Sample Tree
Root Sam Sample Tree (based on correlations of expression profiles)

Root Sam Sample MDS
Root Sam Sample MDS (based on correlations of expression profiles)





Intersect Map
Overlap Map of Present Call Gene Sets [intersect matrix] [Jaccard matrix] [AGI matrix]


go_term_heatmap
GO Term Heatmap
(corresponding table w. mean expression values)

(E) Meta Analysis



(F) Hormone Data Analysis


ChIP-Seq Analysis

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