Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis

Table 3: Type II network, divided ranks. This table presents the output of the simulation of a type-II network in which we relied on the high confidence interactions and micro-array results. The output of the micro-array was then ranked and these ranks used as input into the network simulation. After performing two such simulations (one for the MK5 off and one for the MK5 on microarray output), we divided the ranks and sorted the results accordingly. The output of this technique is a collection of proteins that cluster naturally together.


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Rank Gene Hugo description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 1813 to 1862 of 3228 in total 
Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Hugo	description	red	green	network_comparison	
1813	GALNTL1	similar to expressed sequence ai415388 (fragment). [source:sptrembl;acc:q8n428]	216.854	214.35	1.01168	
1814	PPP1CC	serine/threonine protein phosphatase pp1-gamma catalytic subunit (ec 3.1.3.16) (pp-1g). [source:swissprot;acc:p36873]	122.3	123.727	1.01167	
1815		dpy-30-like protein. [source:swissprot;acc:q9c005]	220.462	217.926	1.01164	
1816	RAB11FIP1	rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [source:refseq;acc:nm_025151]	220.462	217.926	1.01164	
1817	RAB11FIP5	gamma-snap-associated factor 1; rab11-interacting protein. [source:refseq;acc:nm_015470]	220.462	217.926	1.01164	
1818	COX4NB	neighbor of cox4. [source:swissprot;acc:o43402]	220.462	217.926	1.01164	
1819	C14orf122	protein c14orf122 (cgi-112). [source:swissprot;acc:q9y3b6]	220.462	217.926	1.01164	
1820	ATP9A	potential phospholipid-transporting atpase iia (ec 3.6.1.-). [source:swissprot;acc:o75110]	220.462	217.926	1.01164	
1821	RBM38	rna-binding region containing protein 1 (hsrnaseb) (ssdna binding protein seb4) (cll-associated antigen kw-5). [source:swissprot;acc:q9h0z9]	218.36	215.874	1.01152	
1822	PFKL	6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [source:swissprot;acc:p17858]	240.32	243.085	1.01151	
1823	FXR2	fragile x mental retardation syndrome related protein 2. [source:swissprot;acc:p51116]	202.386	200.086	1.0115	
1824	CAPZA1	f-actin capping protein alpha-1 subunit (capz alpha-1). [source:swissprot;acc:p52907]	214.722	212.281	1.0115	
1825	FXR1	fragile x mental retardation syndrome related protein 1. [source:swissprot;acc:p51114]	202.386	200.086	1.0115	
1826	NUP43	nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	202.393	200.094	1.01149	
1827	NME3	nucleoside diphosphate kinase 3 (ec 2.7.4.6) (ndk 3) (ndp kinase 3) (nm23-h3) (dr-nm23). [source:swissprot;acc:q13232]	191.39	189.219	1.01147	
1828	FMR1	fragile x mental retardation 1 protein (protein fmr-1) (fmrp). [source:swissprot;acc:q06787]	202.41	200.115	1.01147	
1829	CAD	cad protein [includes: glutamine-dependent carbamoyl-phosphate synthase (ec 6.3.5.5); aspartate carbamoyltransferase (ec 2.1.3.2); dihydroorotase (ec 3.5.2.3)]. [source:swissprot;acc:p27708]	212.884	215.323	1.01146	
1830	PFKM	6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [source:swissprot;acc:p08237]	240.32	243.069	1.01144	
1831		f-actin capping protein alpha-2 subunit (capz alpha-2). [source:swissprot;acc:p47755]	214.746	212.328	1.01139	
1832	SLC4A1AP	solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [source:refseq;acc:nm_018158]	180.409	182.459	1.01136	
1833	CKS2	cyclin-dependent kinases regulatory subunit 2 (cks-2). [source:swissprot;acc:p33552]	180.409	182.459	1.01136	
1834	CTNNAL1	catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [source:refseq;acc:nm_003798]	180.409	182.459	1.01136	
1835	GORASP2	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [source:refseq;acc:nm_015530]	194.573	192.396	1.01132	
1836	RPIA	ribose 5-phosphate isomerase (ec 5.3.1.6) (phosphoriboisomerase). [source:swissprot;acc:p49247]	208.821	211.17	1.01125	
1837	KHK	ketohexokinase (ec 2.7.1.3) (hepatic fructokinase). [source:swissprot;acc:p50053]	218.984	221.446	1.01124	
1838		purine nucleoside phosphorylase (ec 2.4.2.1) (inosine phosphorylase) (pnp). [source:swissprot;acc:p00491]	218.984	221.446	1.01124	
1839	EIF2S2	eukaryotic translation initiation factor 2 subunit 2 (eukaryotic translation initiation factor 2 beta subunit) (eif-2-beta). [source:swissprot;acc:p20042]	221.525	224.001	1.01118	
1840	APEX1	dna-(apurinic or apyrimidinic site) lyase (ec 4.2.99.18) (ap endonuclease 1) (apex nuclease) (apen) (ref-1 protein). [source:swissprot;acc:p27695]	211.882	209.544	1.01116	
1841	PARL	presenilins associated rhomboid-like protein. [source:refseq;acc:nm_018622]	212.455	210.113	1.01115	
1842	BBOX1	gamma-butyrobetaine,2-oxoglutarate dioxygenase (ec 1.14.11.1) (gamma-butyrobetaine hydroxylase) (gamma-bbh). [source:swissprot;acc:o75936]	212.455	210.113	1.01115	
1843	ATP11A	potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [source:swissprot;acc:p98196]	212.455	210.113	1.01115	
1844	PAX6	paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [source:swissprot;acc:p26367]	214.773	212.417	1.01109	
1845	ABI2	abl-interactor 2; abl-interacting protein 1 (sh3-containing protein); abl binding protein 3; arg protein tyrosine kinase-binding protein; abl-interactor protein 2b; similar to spectrin sh3 domain binding protein 1. [source:refseq;acc:nm_005759]	217.077	214.702	1.01106	
1846	ABI1	spectrin sh3 domain binding protein 1; eps8 binding protein; interactor protein ablbp4; abl-interactor protein 1 long; nap1 binding protein. [source:refseq;acc:nm_005470]	217.066	214.698	1.01103	
1847		brain protein 16. [source:refseq;acc:nm_016458]	216.811	219.195	1.011	
1848	BAAT	bile acid coenzyme a: amino acid n-acyltransferase; glycine n-choloyltransferase. [source:refseq;acc:nm_001701]	218.441	216.064	1.011	
1849	ACOT1	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [source:swissprot;acc:p49753]	218.445	216.074	1.01097	
1850	CAP1	adenylyl cyclase-associated protein 1 (cap 1). [source:swissprot;acc:q01518]	215.931	213.587	1.01097	
1851	ACOT4	peroxisomal acyl-coa thioesterase 2b; likely ortholog of mouse peroxisomal acyl-coa thioesterase 2b. [source:refseq;acc:nm_152331]	218.448	216.08	1.01096	
1852		3-hydroxyisobutyryl-coenzyme a hydrolase. [source:refseq;acc:nm_014362]	196.008	198.154	1.01095	
1853	TTL	tubulin-tyrosine ligase. [source:refseq;acc:nm_153712]	217.924	215.564	1.01095	
1854	EIF2B5	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q13144]	222.215	224.637	1.0109	
1855	GRSF1	g-rich sequence factor-1 (grsf-1). [source:swissprot;acc:q12849]	217.891	215.542	1.0109	
1856	HNRPH3	heterogeneous nuclear ribonucleoprotein h3 (hnrnp h3) (hnrnp 2h9). [source:swissprot;acc:p31942]	217.892	215.543	1.0109	
1857	EIF2B3	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [source:swissprot;acc:q9nr50]	222.215	224.637	1.0109	
1858	HNRPF	heterogeneous nuclear ribonucleoprotein f (hnrnp f). [source:swissprot;acc:p52597]	217.893	215.545	1.01089	
1859	HNRPH1	heterogeneous nuclear ribonucleoprotein h (hnrnp h). [source:swissprot;acc:p31943]	217.895	215.547	1.01089	
1860	HNRPH2	heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [source:swissprot;acc:p55795]	217.895	215.547	1.01089	
1861	CYB5R2	cytochrome b5 reductase b5r.2. [source:refseq;acc:nm_016229]	210.856	213.147	1.01087	
1862	CYB5R1	cytochrome b5 reductase 1 (b5r.1). [source:refseq;acc:nm_016243]	210.856	213.147	1.01087	

Legend:
- Rank is the rank after comparing the two networks
- Hugo is the HGNC identifier if it exists
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/