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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Network Comparison Type	Value Type	Gene	green	description	Rank	network_comparison	red	Filtered	Interaction Map

Results: HTML CSV LaTeX

Showing element 458 to 507 of 3228 in total

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

green	description	Rank	network_comparison	red
0.00001	vacuolar proton-atpase subunit. [sptrembl;acc:q8nhe4]	2821	1	0.00001
	vascular endothelial growth factor a precursor (vegf-a) (vascular permeability factor) (vpf). [swissprot;acc:p15692]	3066
	vascular endothelial growth factor b precursor (vegf-b) (vegf related factor) (vrf). [swissprot;acc:p49765]	2811
	vasopressin-activated calcium-mobilizing receptor (vacm-1) (cullin homolog 5) (cul-5). [swissprot;acc:q93034]	2840
	vesicle transport-related protein isoform a; vesicle transport-related protein. [refseq;acc:nm_016106]	3157
	vesicle-associated membrane protein-associated protein a (vamp- associated protein a) (vamp-a) (vap-a) (33 kda vamp-associated protein) (vap-33). [swissprot;acc:q9p0l0]	3123
	vesicle-associated membrane protein-associated protein b/c (vamp- associated protein b/c) (vamp-b/vamp-c) (vap-b/vap-c). [swissprot;acc:o95292]	3023
	vps28 protein homolog. [swissprot;acc:q9uk41]	2871
	wd-repeat containing protein ciao 1. [swissprot;acc:o76071]	2927
	williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71]	3218
	wnt1 inducible signaling pathway protein 1 isoform 1 precursor; wnt-1 signaling pathway protein 1; wnt1 signaling pathway protein 1; wnt-1 inducible signaling pathway protein 1. [refseq;acc:nm_003882]	3109
	wnt1 inducible signaling pathway protein 3 isoform 1; wnt-1 signaling pathway protein 3; wnt1 signaling pathway protein 3; wnt-1 inducible signaling pathway protein 3. [refseq;acc:nm_003880]	3065
	xanthine dehydrogenase/oxidase [includes: xanthine dehydrogenase (ec 1.1.1.204) (xd); xanthine oxidase (ec 1.1.3.22) (xo) (xanthine oxidoreductase)]. [swissprot;acc:p47989]	2882
	zinc finger daz interacting protein 1. [refseq;acc:nm_014934]	2981
	zinc transporter 1 (znt-1). [swissprot;acc:q9y6m5]	2822
	zinc transporter 3 (znt-3). [swissprot;acc:q99726]	3049
24	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	1	2.4	10
28	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	3	1.86667	15
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	4
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	6
	cytohesin 4. [swissprot;acc:q9uia0]	5
	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]	2
42.3003	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	147	1.2009	50.7983
44	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5]	23	1.31818	58
	mitochondrial solute carrier protein. [refseq;acc:nm_145305]	27
	pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04]	24
	pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23]	25
	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	26
46	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	152	1.19565	55
	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	150
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	151
49	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	143	1.20408	59
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	140
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	142
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	141
75.3531	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936]	14	1.32952	56.6768
75.3948	microtubule-associated proteins 1a/1b light chain 3b (map1a/map1b lc3 b) (map1a/1b light chain 3 b). [swissprot;acc:q9gzq8]	15	1.32914	56.7244
75.3954	microtubule-associated proteins 1a/1b light chain 3a (map1a/map1b lc3 a) (map1a/1b light chain 3 a). [swissprot;acc:q9h492]	16	1.32913	56.7252
75.447	cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326]	17	1.32866	56.7841
78.8995	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	322	1.09948	86.7483
83.0461	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	48	1.26868	65.4586
97.4011	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	592	1.06298	91.63
98.0548	apg3p; pc3-96 protein. [refseq;acc:nm_022488]	169	1.18722	82.5916
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	168
101.613	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	397	1.08932	110.689
105	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	52	1.26667	133
	beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407]	50
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	49
	spermatogenesis associated 6. [refseq;acc:nm_019073]	51
110.265	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	88	1.24949	88.2482

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
- 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.