figure s1. raw output of pca clustering of tissues. a two · 2016. 3. 8. · figure s1. raw output...

3

Figure S1. Raw output of PCA clustering of tissues. A: Three significantly separated clusters of total 26 studied tissues. B: Two significantly separated clusters of studied tissues without epithelial (skin and tonsil) and reference (muscle and liver) tissues. Cluster boundary significance testing is performed based on K-mean clustering and bivariate t-distribution using stat_ellipse package (https://github.com/JoFrhwld/FAAV/blob/master/r/stat-ellipse.R) and presented in ggplot2 in R.

Upload: others

Post on 13-Aug-2021

5 views

Category:

Documents

0 download

Report

Download

Embed Size (px):

TRANSCRIPT

Page 1: Figure S1. Raw output of PCA clustering of tissues. A Two · 2016. 3. 8. · Figure S1. Raw output of PCA clustering of tissues. A: Three significantly separated clusters of total

Figure S1. Raw output of PCA clustering of tissues. A: Three significantly separated clusters of total 26 studied tissues. B: Two significantly separated clusters of studied tissues without epithelial (skin and tonsil) and reference (muscle and liver) tissues. Cluster boundary significance testing is performed based on K-mean clustering and bivariate t-distribution using stat_ellipse package (https://github.com/JoFrhwld/FAAV/blob/master/r/stat-ellipse.R) and presented in ggplot2 in R.

Page 2: Figure S1. Raw output of PCA clustering of tissues. A Two · 2016. 3. 8. · Figure S1. Raw output of PCA clustering of tissues. A: Three significantly separated clusters of total

Figure S2. Expression profile of gastrointestine related keratin genes. Keratin genes are selected based on their average count per million values in gastrointestinal tissues > 3.

Page 3: Figure S1. Raw output of PCA clustering of tissues. A Two · 2016. 3. 8. · Figure S1. Raw output of PCA clustering of tissues. A: Three significantly separated clusters of total

Figure S3. Clustering of transporter genes. Genes in boxes are assigned with sheep clusters as shown in table S1.

Dimension reduction : PCA and Clustering Christopher Workman Center for Biological Sequence Analysis DTU

A NEW ENTERPRISE SCALE SOFTWARE SYSTEM FOR … · gene clustering, and PCA/ICA based ... K-means and hierarchical clustering and dendrogram ... grid that can expand to any number

Scalable Probabilistic PCA - ww2.amstat.org › meetings › sdss › 2018 › online... · Scalable Probabilistic PCA PCA Probabilistic PCA Results Probabilistic PCA EM algorithm:

Machine Learning: Think Big and Parallel - Day 2 · Unsupervised Learning | day2 Clustering: k-means, Spectral Clustering Dimensionality Reduction: PCA, Matrix Factorization for Recommender

Regional Pattern Discovery in Geo-Referenced Datasets ...ceick/kdd/CEO09.pdfSpatial Data Mining, Correlation Patterns, Regional Knowledge Discovery, Clustering, PCA. 1 Introduction

PCA-6179 - Advantechdownloadt.advantech.com › ... › 1-A39G0 › PCA6179_ed1.pdf · PCA-6179 Series comparison table Model PCA-6179L PCA-6179V PCA-6179VE PCA-6179VS PCA-6179F CPU:

Turning Big Data into Tiny Data: Constant-size Coresets for K-means, PCA and Pojective Clustering

Part 2. Spectral Clustering from Matrix Perspectivestaff.ustc.edu.cn/.../matrix-factorization/PCA-tutor2.pdf• Chung, 1997, Spectral graph theory book • Shi & Malik, 2000, Normalized

LECTURE 3 Introduction to PCA and PLS K-mean clustering

Variable Clustering and Mixed Data. The ClustOfVar · PDF fileThe package ClustOfVar ... PCA (Principal Component Analysis) fornumericaldata, MCA (Multiple Correspondence Analysis

LECTURE 3 Introduction to PCA and PLS K-mean clustering Protein function prediction using network concepts Network Centrality measures

Influential Features PCA for high dimensional clustering

PCA Extension By Jonash. Outline Robust PCA Generalized PCA –Clustering points on a line –Clustering lines on a plane –Clustering hyperplanes in a space

Clustering and Principal Component Methods - Freefactominer.free.fr/more/tutorial_2010_clustering.pdf · Clustering and Principal Component Methods ... PCA as a preprocessing

Spectral Clustering Based on Local PCA · We propose a spectral clustering method based on local principal components analysis (PCA). After performing local PCA in selected neighborhoods,

Clustering by Important Features PCA (IF-PCA)jiashun/Research/Talks/Medallion.pdfI CV: not directly implementable (class labels unknown) I FDR: need tuning and target on Rare/Strong

Dimension reduction : PCA and Clustering

Recitation Clustering and PCA Colin White Nupur Chatterji, Kenny …ninamf/courses/401sp18/recitations... · 2018-04-19 · 3 of 42 Applications (Clustering comes up everywhere

PCA, Clustering and Classificationpca.narod.ru/pcaclustclass.pdf · PCA, Clustering and Classification ... Pat1 Pat2 Pat3 Pat4 Pat5 Pat6 Pat7 Pat8 Pat9 ... 204891_s_at 78 71 152 74

PhD Courseedu.sablab.net/abs2016/pdf/AdvBiostat_L6.pdf · 3. Statistical TestsL4. Linear L5. PCA, Clustering and ClassificationL6. Data analysis in transcriptomicsmodels edu.sablab.net/abs2016

Principal Component Analysis (PCA) for Clustering Gene Expression Data K. Y. Yeung and W. L. Ruzzo

PCA, Clustering and Classification - · PDF filePCA, Clustering and Classification ... Pat1 Pat2 Pat3 Pat4 Pat5 Pat6 Pat7 Pat8 Pat9 ... 207820_at 63 43 53 97 102 54 75 48 30 75

Analytical Techniques Data Driven Principal Component Analysis (PCA) Independent Component Analysis (ICA) Fuzzy Clustering Others Structural equation modeling

Robust PCA Robust PCA 3: Spherical PCA. Robust PCA

Spectral Algorithms for Learning and Clustering: PCA and Beyond

Tissues Epithelial Tissues Connective Tissues Muscle Tissues Nervous Tissues

Dimension reduction : PCA and Clustering - CBS · Dimension reduction : PCA and Clustering By Hanne Jarmer Slides by Christopher Workman Center for Biological Sequence Analysis DTU

Image Segmentation using clustering (Texture with PCA)

Optimal solutions for Sparse Principal Component Analysisfbach/SPO.pdf · Clustering of the gene expression data in the PCA versus sparse PCA basis with 500 genes. The factors f on

PCA, Clustering and Classification by Agnieszka S. Juncker

Introduction to Multivariate Image Analysis (MIA) · PDF fileMATLAB for Chemometricians Chemometrics I -- PCA Chemometrics II -- Regression and PLS Clustering and Classification Advanced

PCA, Clustering and Classification by Agnieszka S. Juncker Part of the slides is adapted from Chris Workman

Spectral Clustering Based on Local PCAjmlr.csail.mit.edu/papers/volume18/14-318/14-318.pdf · 2020-05-22 · Spectral Clustering Based on Local PCA in more detail later on. In fact,

ABSTRACT - repository.lib.ncsu.edu · ABSTRACT MANGUM, AMANDA JEAN. Self-Organizing Maps for Data Clustering in Acoustic Radiation Force Ultrasound Imaging of Cardiovascular Tissues

PCA-6180 - Advantechdownloadt.advantech.com/ProductFile/Downloadfile4/1-YZ4N/6180... · PCA-6180 Series comparison table Model PCA-6180E PCA-6180E2 PCA-6180SE PCA-6180F CPU: Intel