Analysis Results
by
Thomas Girke
—
last modified
Jul 19, 2014 01:48 AM
(A) Sample Clustering
Fig 1. Sample Tree: Clustering of all cell samples (CEL files)
Download correlation matrix (method: Spearman).

Fig2. Hierarchical Clustering with Heatmap
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

Intersect Map of Enrichment Gene Sets (intersect matrix)

OL Mean Expression (Row Scale)

OL Mean Expression (Col Scale)
Fig3 A. Fuzzy Clustering: K=22
Tabular results in above master table.
Corresponding GO results for clusters.

Download correlation matrix (method: Spearman).
(B) Gene Clustering

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

Intersect Map of Enrichment Gene Sets (intersect matrix)

OL Mean Expression (Row Scale)

OL Mean Expression (Col Scale)
- GO Results for Enrichment Sets in heatTable
- Benfey Enrichment Data
- Pairwise Enrichment Data
- Motif discovery for pairwise DEG sets [Stats Table]
- Enrichment of AGRIS motifs in DEG sets (Corresponding AGI List)

Fig3 A. Fuzzy Clustering: K=22
Tabular results in above master table.
Corresponding GO results for clusters.
Motif Discovery for Fuzzy Clustering K=22
- CL1: Weeder results: click here.
- CL2: Weeder results: click here.
- CL3: Weeder results: click here.
- CL4: Weeder results: click here.
- CL5: Weeder results: click here.
- CL6: Weeder results: click here.
- CL7: Weeder results: click here.
- CL8: Weeder results: click here.
- CL9: Weeder results: click here.
- CL10: Weeder results: click here.
- CL11: Weeder results: click here.
- CL12: Weeder results: click here.
- CL13: Weeder results: click here.
- CL14: Weeder results: click here.
- CL15: Weeder results: click here.
- CL16: Weeder results: click here.
- CL17: Weeder results: click here.
- CL18: Weeder results: click here.
- CL19: Weeder results: click here.
- CL20: Weeder results: click here.
- CL21: Weeder results: click here.
- CL22: Weeder results: click here.

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

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

Fig3 C. Fuzzy Clustering: K=10
Corresponding GO results for clusters.
(C.1) DEG and Motif Analysis of HMGp, GL2p and L1p

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
agris_Ram_CLV3p_FILp_KANp_LASp.xls
(C.2) Layers: DEG and Motif Analysis of HMGp, GL2p, L1p and WUSp
GO Results for Enrichment Sets in heatTable
(C.3) Zones: DEG and Motif Analysis of CLV3p, LASp, and KANp
GO Results for Enrichment Sets in heatTable
(D) Root-SAM Comparisons
(E) Meta Analysis
(F) Hormone Data Analysis
ChIP-Seq Analysis
Peak Calling (extended reads to 200bp)
Peak Calling (unextended read)
Peak Calling New June 16 (several methods)
simple_comb_sig_bgr.xls June 23
simple_sig1.xls June 23
simple_sig2.xls June 23
sig1_bayespeak.xls June 23
sig1_bgr1_bayespeak.xls June 23
sig1_bgr2_bayespeak.xls June 23
sig2_bayespeak.xls June 23
sig2_bgr1_bayespeak.xls June 23
sig2_bgr2_bayespeak.xls June 23
Overlaps among peak sets (olMA.xls) June 24
Motifs


- HMGp Set (Sequences) Weeder results: click here; PWM Table
- GL2p Set (Sequences) Weeder results: click here; PWM Table
- L1p (Sequences) Weeder results: click here; PWM Table
Ram's Final Motif Discovery (May 18, 2011)
HMGp_GL2p_WUSp_statsDF.xls- HMGp Set (Sequences) Weeder results: click here; PWM Table
- GL2p Set (Sequences) Weeder results: click here; PWM Table
- WUSp Set (Sequences) Weeder results: click here; PWM Table
CLV3p_FILp_KANp_LASp_statsDF.xls
- CLV3p Set (Sequences) Weeder results: click here; PWM Table
- FILp Set (Sequences) Weeder results: click here; PWM Table
- KANp Set (Sequences) Weeder results: click here; PWM Table
- LASp Set (Sequences) Weeder results: click here; PWM Table
Ram's Final Agris Motif Finding (May 19, 2011)
agris_Ram_HMGp_GL2p_WUSp.xlsagris_Ram_CLV3p_FILp_KANp_LASp.xls
(C.2) Layers: DEG and Motif Analysis of HMGp, GL2p, L1p and WUSp

GO Results for Enrichment Sets in heatTable
Motif Discovery
Motif Searches in 1kb upstream of DEGs.- HMGp Set (Sequences) Weeder results: click here.
- GL2p Set (Sequences) Weeder results: click here.
- L1p (Sequences) Weeder results: click here.
- WUSp (Sequences) Weeder results: click here.
Motif Finding
- Enrichment of Agris motifs
- agris_TwoOL_LASp_KANp_FILp_CLV3p_WUSp_S17Sp_AtHB8
- agris_TwoOL_HMGp_GL2p_L1p_WUSp_
(C.3) Zones: DEG and Motif Analysis of CLV3p, LASp, and KANp

GO Results for Enrichment Sets in heatTable
Motif Discovery
Motif Searches in 1kb upstream of DEGs.- CLV3p Set (Sequences) Weeder results: click here.
- KANp Set (Sequences) Weeder results: click here.
- LASp (Sequences) Weeder results: click here.
Motif Finding
Enrichment of Agris motifs(D) Root-SAM Comparisons
Root Sam Sample Tree (based on correlations of expression profiles)

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


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

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

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

GO Term Heatmap
(corresponding table w. mean expression values)
(E) Meta Analysis
- Meta Analysis Table (Oct 6, 2010)
(F) Hormone Data Analysis
ChIP-Seq Analysis
Peak Calling (extended reads to 200bp)
Peak Calling (unextended read)
Peak Calling New June 16 (several methods)
simple_comb_sig_bgr.xls June 23
simple_sig1.xls June 23
simple_sig2.xls June 23
sig1_bayespeak.xls June 23
sig1_bgr1_bayespeak.xls June 23
sig1_bgr2_bayespeak.xls June 23
sig2_bayespeak.xls June 23
sig2_bgr1_bayespeak.xls June 23
sig2_bgr2_bayespeak.xls June 23
Overlaps among peak sets (olMA.xls) June 24
Motifs


