MK5 Microarray Data

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

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Showing element 2625 to 2674 of 3228 in total

Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	Hugo	description	red	green	network_comparison
2625	WTAP	wilms' tumor 1-associating protein (wt1-associated protein). [swissprot;acc:q15007]	204.304	204.028	1.00135
2626	ACTR2	actin-like protein 2 (actin-related protein 2). [swissprot;acc:o15142]	224.891	225.195
2627	COG3	conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2]
2628	ACTR3B	similar to actin-related protein 3-beta. [sptrembl;acc:q96bt2]
2629	ARPC1B	arp2/3 complex 41 kda subunit (p41-arc) (actin-related protein 2/3 complex subunit 1b). [swissprot;acc:o15143]
2630	ZMYM2	zinc finger protein 198 (fused in myeloproliferative disorders protein) (rearranged in atypical myeloproliferative disorder protein). [swissprot;acc:q9ubw7]
2631	ACTR3	actin-like protein 3 (actin-related protein 3) (actin-2). [swissprot;acc:p32391]
2632	ARPC3	arp2/3 complex 21 kda subunit (p21-arc) (actin-related protein 2/3 complex subunit 3). [swissprot;acc:o15145]
2633	NRD1	nardilysin precursor (ec 3.4.24.61) (n-arginine dibasic convertase) (nrd convertase) (nrd-c). [swissprot;acc:o43847]
2634	ARPC1A	actin-related protein 2/3 complex subunit 1a (sop2-like protein). [swissprot;acc:q92747]
2635	CLP1	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	166.612	166.393	1.00132
2636	ANAPC11	anaphase promoting complex subunit 11 (hepatocellular carcinoma associated ring finger protein) (hspc214). [swissprot;acc:q9nyg5]	195.635	195.384	1.00128
2637	no value	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	187.075	186.84	1.00126
2638	F11R	junctional adhesion molecule 1 precursor (jam) (platelet adhesion molecule 1) (pam-1) (platelet f11 receptor). [swissprot;acc:q9y624]	204.911	205.168	1.00125
2639	MYO7A	myosin viia. [swissprot;acc:q13402]	220.658	220.386	1.00123
2640	UBE2B	ubiquitin-conjugating enzyme e2 b (ec 6.3.2.19) (ubiquitin-protein ligase b) (ubiquitin carrier protein b) (hr6b) (hhr6b) (e2-17 kda). [swissprot;acc:p23567]
2641	UBE2A	ubiquitin-conjugating enzyme e2 a (ec 6.3.2.19) (ubiquitin-protein ligase a) (ubiquitin carrier protein a) (hr6a) (hhr6a). [swissprot;acc:p49459]
2642	TOPBP1	topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027]	194.097	194.328	1.00119
2643	ACOX1	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
2644	ATP5J2	atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]
2645	DHX35	probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]
2646	TSC22D4	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8]	213.169	213.417	1.00116
2647	MAT1A	s-adenosylmethionine synthetase alpha and beta forms (ec 2.5.1.6) (methionine adenosyltransferase) (adomet synthetase) (mat-i/iii). [swissprot;acc:q00266]	212.496	212.25
2648	DEGS1	sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676]	213.169	213.417
2649	no value	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]	213.63	213.874	1.00114
2650	KHSRP	kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685]	217.188	216.942	1.00113
2651	NFKBIE	nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [swissprot;acc:o00221]	201.37	201.594	1.00111
2652	NFKB1	nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [swissprot;acc:p19838]	201.451	201.673	1.0011
2653	NFKBIB	nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [swissprot;acc:q15653]	201.452	201.674
2654	NFKB2	nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [swissprot;acc:q00653]
2655	BCL3	b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]	201.445	201.667
2656	FUBP1	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	217.179	216.943	1.00109
2657	DLG2	channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	216.934	216.7	1.00108
2658	DLG4	presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352]	216.933
2659	DLG3	presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796]
2660	DLG1	presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959]	216.937	216.704
2661	FES	proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332]	204.768	204.549	1.00107
2662	MOCS2	molybdenum cofactor synthesis protein 2 large subunit (molybdopterin synthase large subunit) (mpt synthase large subunit) (mocs2b) (moco1- b). [swissprot;acc:o96007]
2663	ANAPC10	anaphase-promoting complex subunit 10; anaphase-promoting complex 10. [refseq;acc:nm_014885]
2664	RPL29	60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914]
2665	FER	proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591]
2666	TXNDC1	thioredoxin domain containing; thioredoxin-related transmembrane protein; thioredoxin domain-containing. [refseq;acc:nm_030755]	210.136	209.911
2667	MOCS3	molybdenum cofactor synthesis protein 3 (molybdopterin synthase sulfurylase) (mpt synthase sulfurylase). [swissprot;acc:o95396]	204.768	204.549
2668	FUBP3	fuse binding protein 3 (fragment). [sptrembl;acc:q92946]	217.176	216.944
2669	GPD1	glycerol-3-phosphate dehydrogenase [nad+], cytoplasmic (ec 1.1.1.8) (gpd-c) (gpdh-c). [swissprot;acc:p21695]	214.575	214.354	1.00103
2670	KRAS	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	144.391	144.538	1.00102
2671	GNPNAT1	similar to glucosamine-phosphate n-acetyltransferase (hypothetical protein flj33258). [sptrembl;acc:q96ek6]	216.288	216.067
2672	BCAT1	branched-chain amino acid aminotransferase, cytosolic (ec 2.6.1.42) (bcat(c)) (eca39 protein). [swissprot;acc:p54687]	210.957	210.741
2673	RAD9A	rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584]	216.372	216.588	1.001
2674	GLUL	glutamine synthetase (ec 6.3.1.2) (glutamate--ammonia ligase). [swissprot;acc:p15104]	203.151	202.948

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- 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.