Supplementary website for

DEGAS: De novo discovery of dysregulated pathways in human diseases

Igor Ulitsky^1,*, Akshay Krishnamurthy², Richard M. Karp³, and Ron Shamir¹

¹ Blavatnik School of Computer Science, Tel Aviv University, Tel Aviv 69978, Israel.
² University of California, Berkeley, University Avenue, Berkeley, CA 94720
³ International Computer Science Institute, 1947 Center St., Berkeley, CA 94704
^* Current address: Whitehead Institute for Biomedical Research, 9 Cambridge Center, Cambridge MA, USA 02142

An implementation of DEGAS which can be applied to network and gene expression data is available as part of MATISSE

. Each of the resulting dysregulated pathways listed below can be loaded in MATISSE as a session .zip file which contains all the relevant information, including network topology, gene expression, annotations etc.

Disease dysregulated pathways:

Dataset	Disease (KEGG)	Data	Direction	MATISSE session	k	Size	Genes	Network	Raw data	Expression Heatmap	Dysregulation matrix	Dysregulation Heatmap
HD	Huntington's disease	GEO	Down regulated	session .zip file	20	30	Gene list	.sif file	Text file	Image	Text file	Image
HD	Huntington's disease	GEO	Differentially expressed	session .zip file	15	21	Gene list	.sif file	Text file	Image	Text file	Image
HD	Huntington's disease	GEO	Up regulated	session .zip file	30	61	Gene list	.sif file	Text file	Image	Text file	Image
SLE	Systemic lupus erythematosus	GEO	Down regulated	session .zip file	15	30	Gene list	.sif file	Text file	Image	Text file	Image
SLE	Systemic lupus erythematosus	GEO	Differentially expressed	session .zip file	30	68	Gene list	.sif file	Text file	Image	Text file	Image
SLE	Systemic lupus erythematosus	GEO	Up regulated	session .zip file	25	60	Gene list	.sif file	Text file	Image	Text file	Image
SUN-GLIOBLASTOMA	Pathways in cancer	GEO	Down regulated	session .zip file	20	20	Gene list	.sif file	Text file	Image	Text file	Image
SUN-GLIOBLASTOMA	Pathways in cancer	GEO	Differentially expressed	session .zip file	25	26	Gene list	.sif file	Text file	Image	Text file	Image
SUN-GLIOBLASTOMA	Pathways in cancer	GEO	Up regulated	session .zip file	30	30	Gene list	.sif file	Text file	Image	Text file	Image
SUN-ASTROCYTOMA	Pathways in cancer	GEO	Down regulated	session .zip file	5	5	Gene list	.sif file	Text file	Image	Text file	Image
SUN-ASTROCYTOMA	Pathways in cancer	GEO	Differentially expressed	session .zip file	15	16	Gene list	.sif file	Text file	Image	Text file	Image
SUN-ASTROCYTOMA	Pathways in cancer	GEO	Up regulated	session .zip file	15	16	Gene list	.sif file	Text file	Image	Text file	Image
SUN-OLIGODENDROGLIOMA	Pathways in cancer	GEO	Down regulated	session .zip file	10	10	Gene list	.sif file	Text file	Image	Text file	Image
SUN-OLIGODENDROGLIOMA	Pathways in cancer	GEO	Differentially expressed	session .zip file	10	10	Gene list	.sif file	Text file	Image	Text file	Image
SUN-OLIGODENDROGLIOMA	Pathways in cancer	GEO	Up regulated	session .zip file	25	27	Gene list	.sif file	Text file	Image	Text file	Image
ESTILO-OTSCC	Pathways in cancer	GEO	Down regulated	session .zip file	30	87	Gene list	.sif file	Text file	Image	Text file	Image
ESTILO-OTSCC	Pathways in cancer	GEO	Differentially expressed	session .zip file	20	41	Gene list	.sif file	Text file	Image	Text file	Image
ESTILO-OTSCC	Pathways in cancer	GEO	Up regulated	session .zip file	30	56	Gene list	.sif file	Text file	Image	Text file	Image
YE-OTSCC	Pathways in cancer	GEO	Down regulated	session .zip file	5	8	Gene list	.sif file	Text file	Image	Text file	Image
YE-OTSCC	Pathways in cancer	GEO	Differentially expressed	session .zip file	25	37	Gene list	.sif file	Text file	Image	Text file	Image
YE-OTSCC	Pathways in cancer	GEO	Up regulated	session .zip file	30	51	Gene list	.sif file	Text file	Image	Text file	Image
MORAN-PD	Parkinson's disease	GEO	Down regulated	session .zip file	30	67	Gene list	.sif file	Text file	Image	Text file	Image
MORAN-PD	Parkinson's disease	GEO	Differentially expressed	session .zip file	30	64	Gene list	.sif file	Text file	Image	Text file	Image
MORAN-PD	Parkinson's disease	GEO	Up regulated	session .zip file	30	73	Gene list	.sif file	Text file	Image	Text file	Image
LESNICK-PD	Parkinson's disease	GEO	Down regulated	session .zip file	5	7	Gene list	.sif file	Text file	Image	Text file	Image
LESNICK-PD	Parkinson's disease	GEO	Differentially expressed	session .zip file	30	48	Gene list	.sif file	Text file	Image	Text file	Image
LESNICK-PD	Parkinson's disease	GEO	Up regulated	session .zip file	25	37	Gene list	.sif file	Text file	Image	Text file	Image
ASTHMA	Asthma	GEO	Down regulated	session .zip file	30	139	Gene list	.sif file	Text file	Image	Text file	Image
ASTHMA	Asthma	GEO	Differentially expressed	session .zip file	30	109	Gene list	.sif file	Text file	Image	Text file	Image
ASTHMA	Asthma	GEO	Up regulated	session .zip file	25	102	Gene list	.sif file	Text file	Image	Text file	Image
AD	Alzheimer's disease	GEO	Down regulated	session .zip file	25	25	Gene list	.sif file	Text file	Image	Text file	Image
AD	Alzheimer's disease	GEO	Differentially expressed	session .zip file	30	30	Gene list	.sif file	Text file	Image	Text file	Image
AD	Alzheimer's disease	GEO	Up regulated	session .zip file	30	30	Gene list	.sif file	Text file	Image	Text file	Image
PYLORI	Epithelial cell signaling in Helicobacter pylori infection	GEO	Down regulated	session .zip file	15	20	Gene list	.sif file	Text file	Image	Text file	Image
PYLORI	Epithelial cell signaling in Helicobacter pylori infection	GEO	Differentially expressed	session .zip file	20	23	Gene list	.sif file	Text file	Image	Text file	Image
PYLORI	Epithelial cell signaling in Helicobacter pylori infection	GEO	Up regulated	session .zip file	20	22	Gene list	.sif file	Text file	Image	Text file	Image

For questions, contact Igor Ulitsky

Supplementary website for

DEGAS: De novo discovery of dysregulated pathways in human diseases

Igor Ulitsky1,*, Akshay Krishnamurthy2, Richard M. Karp3, and Ron Shamir1

An implementation of DEGAS which can be applied to network and gene expression data is available as part of MATISSE

Disease dysregulated pathways:

Igor Ulitsky^1,*, Akshay Krishnamurthy², Richard M. Karp³, and Ron Shamir¹