PHBI | SY Chan Lab

Computational Analyses

EDDY-PHBI

Stearman RS, Bui QM, Speyer G, Handen A, Cornelius AR, Graham BB, Kim S, Mickler EA, Tuder RM, Chan SY, Geraci MW. Systems Analysis of the Human Pulmonary Arterial Hypertension Lung Transcriptome. American Journal of Respiratory Cell and Molecular Biology. 2018. Epub ahead of print. https://doi.org/10.1165/rcmb.2018-0368OC PMID 30562042.

25 FD vs 58 PAH

Pathway	DB	# genes	p-val	JS	New Dependency	Rewiring	Essentiality Mediators	Specificity Mediators
FORMATION OF ATP BY CHEMIOSMOTIC COUPLING	R	16	0.0053	0.9675	0.00	0.62	ATP5H ATP5A1 ATP5C1 ATP5B
MITOCHONDRIAL TRNA AMINOACYLATION	R	21	0.0084	0.9882	0.47	0.80	VARS2 CARS2 HARS2
TGF BETA RECEPTOR SIGNALING IN EMT EPITHELIAL TO MESENCHYMAL TRANSITION	R	16	0.0104	0.9441	0.00	0.79	ARHGEF18 CGN
TRANSLOCATION OF ZAP 70 TO IMMUNOLOGICAL SYNAPSE	R	14	0.0164	0.9220	0.00	0.46	HLA-DQA1 ZAP70	CD3E CD4
RNA POL I TRANSCRIPTION INITIATION	R	25	0.0231	0.9705	0.08	0.72	GTF2H3 CDK7 GTF2H4	RRN3
CDC6 ASSOCIATION WITH THE ORC ORIGIN COMPLEX	R	11	0.0268	0.9471	0.14	0.75	ORC1
DCC MEDIATED ATTRACTIVE SIGNALING	R	13	0.0296	0.9604	0.04	0.67	DOCK1 WASL NTN1
AMINO ACID SYNTHESIS AND INTERCONVERSION TRANSAMINATION	R	17	0.0337	0.9196	0.65	0.68	PYCR1 PHGDH
ACTIVATION OF IRF3 IRF7 MEDIATED BY TBK1 IKK EPSILON	R	14	0.0341	0.9647	0.05	0.89	TLR3 TICAM1 RPS27A
TRNA AMINOACYLATION	R	42	0.0342	0.9669	0.42	0.57	DARS MARS VARS2 YARS YARS2 EPRS	CARS2 MARS2 TARS2 VARS2 SARS2 NARS2 FARS2 PARS2 IARS2 LARS2 WARS2 AARS2 QARS
RESOLUTION OF AP SITES VIA THE SINGLE NUCLEOTIDE REPLACEMENT	R	12	0.0348	0.9819	0.43	1.00	MPG LIG3
MRNA DECAY BY 3 TO 5 EXORIBONUCLEASE	R	11	0.0382	0.9380	0.06	0.71	EXOSC6
REGULATION OF HYPOXIA INDUCIBLE FACTOR HIF BY OXYGEN	R	25	0.0383	0.9864	0.14	0.78	RBX1 CREBBP HIF3A
PHOSPHORYLATION OF CD3 AND TCR ZETA CHAINS	R	16	0.0421	0.8915	0.00	0.57	LCK CD4	CD3E
ACTIVATED TAK1 MEDIATES P38 MAPK ACTIVATION	R	18	0.0482	0.9482	0.16	0.75	RIPK2 MAP3K7 IRAK2
MTORC1 MEDIATED SIGNALLING	R	11	0.0489	0.9736	0.12	0.81	EIF4E
MITOCHONDRIAL FATTY ACID BETA OXIDATION	R	14	0.0548	0.9271
SIGNAL REGULATORY PROTEIN SIRP FAMILY INTERACTIONS	R	12	0.0578	0.9175
YAP1 AND WWTR1 TAZ STIMULATED GENE EXPRESSION	R	24	0.0605	0.9899
ADP SIGNALLING THROUGH P2RY12	R	21	0.0619	0.9807
ETHANOL OXIDATION	R	10	0.0661	0.9556
SYNTHESIS OF PE	R	11	0.0682	0.9762
THE ROLE OF NEF IN HIV1 REPLICATION AND DISEASE PATHOGENESIS	R	28	0.0705	0.9723
TRANSFERRIN ENDOCYTOSIS AND RECYCLING	R	25	0.0713	0.9779
DSCAM INTERACTIONS	R	11	0.0772	0.8513
G BETA GAMMA SIGNALLING THROUGH PI3KGAMMA	R	25	0.0794	0.9773
ROLE OF SECOND MESSENGERS IN NETRIN1 SIGNALING	R	11	0.0815	0.9654
INFLAMMASOMES	R	17	0.0838	0.9799
TRAF3 DEPENDENT IRF ACTIVATION	R	14	0.0875	0.9435
RNA POL I TRANSCRIPTION TERMINATION	R	22	0.0895	0.8987
E2F ENABLED INHIBITION OF PRE REPLICATION COMPLEX FORMATION	R	10	0.0910	0.9107
REGULATION OF KIT SIGNALING	R	17	0.0926	0.9504
GLYCOSPHINGOLIPID METABOLISM	R	38	0.0937	0.9850
REGULATION OF SIGNALING BY CBL	R	18	0.0955	0.9639
OXYGEN DEPENDENT PROLINE HYDROXYLATION OF HYPOXIA INDUCIBLE FACTOR ALPHA	R	18	0.0969	0.9557
NEF MEDIATES DOWN MODULATION OF CELL SURFACE RECEPTORS BY RECRUITING THEM TO CLATHRIN ADAPTERS	R	21	0.0978	0.9651
ORGANIC CATION ANION ZWITTERION TRANSPORT	R	13	0.0987	0.9883
METABOLISM OF POLYAMINES	R	15	0.0999	0.9622