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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 2630 to 2679 of 66312 in total

Filtered  : 1

Rank	description	Network Comparison Type	Value Type	Interaction Map	red	green	network_comparison
165	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Divided	Rooted	High confidence	55.6486	65.1478	1.1707
	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]		Measured		23693.7	18263	1.29736
	monocarboxylate transporter 3 (mct 3). [swissprot;acc:o95907]			Low confidence	10341.7	11198.5	1.08285
	musashi 1. [refseq;acc:nm_002442]	Subtracted	Rooted	High confidence	54.9787	66.2416	11.2629
	nuclear factor erythroid 2 related factor 2 (nf-e2 related factor 2) (nfe2-related factor 2) (nuclear factor, erythroid derived 2, like 2) (hebp1). [swissprot;acc:q16236]	Divided	Squared	Low confidence	37094.3	41487.9	1.11844
	phospholipase a-2-activating protein (plap) (pla2p). [swissprot;acc:q9y263]	Subtracted	Measured		11162	10526.2	635.8
	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]		Squared		54208.6	48413.8	5794.8
	septin 6. [swissprot;acc:q14141]	Divided	Rooted		97.7187	104.263	1.06697
	spermatogenesis associated 6. [refseq;acc:nm_019073]	Subtracted	Ranked	High confidence	133	105	28
	tetranectin precursor (tn) (plasminogen-kringle 4 binding protein). [swissprot;acc:p05452]		Squared		59016.1	75486.9	16470.8
	tho complex 3. [refseq;acc:nm_032361]		Rooted	Low confidence	72.7219	77.3133	4.5914
166	beta-1,4 mannosyltransferase. [refseq;acc:nm_019109]		Measured		9012.1	8376.35	635.75
	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]		Squared	High confidence	69201.8	53013.4	16188.4
	calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655]	Divided	Ranked	Low confidence	222.502	210.342	1.05781
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]	Subtracted	Squared		53479.8	47812.1	5667.7
	gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747]	Divided	Ranked	High confidence	209.299	249.187	1.19058
	glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737]	Subtracted	Measured		4489.19	2765.82	1723.37
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Divided	Squared		173408	242989	1.40126
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]		Rooted		55.6495	65.1458	1.17064
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]		Measured		23693.7	18263	1.29736
	monocarboxylate transporter 4 (mct 4) (mct 3). [swissprot;acc:o15427]			Low confidence	10325	11178.2	1.08263
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Subtracted	Ranked	High confidence	312	284	28
	nuclear protein ukp68. [refseq;acc:nm_024824]		Rooted		54.9787	66.2416	11.2629
	transcription regulator protein bach2 (btb and cnc homolog 2). [swissprot;acc:q9byv9]	Divided	Squared	Low confidence	37094.3	41487.9	1.11844
	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748]	Subtracted	Ranked		219.336	207.703	11.633
	tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881]		Rooted		87.7928	92.3802	4.5874
	ubiquitin-activating enzyme e1c (uba3 homolog, yeast); ubiquitin-activating enzyme e1c (homologous to yeast uba3). [refseq;acc:nm_003968]	Divided			72.46	77.3071	1.06689
167	amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]	Subtracted	Ranked	High confidence	133	105	28
	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]		Squared		64975.9	81151.2	16175.3
	cyclic-amp-dependent transcription factor atf-3 (activating transcription factor 3). [swissprot;acc:p18847]	Divided		Low confidence	23804.2	26534	1.11468
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]		Measured		12376.5	11436.5	1.08219
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Subtracted	Rooted	High confidence	55.6161	66.7332	11.1171
	glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259]	Divided	Ranked		209.299	249.187	1.19058
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]		Squared		173408	242989	1.40126
	homeobox protein nkx-6.1. [swissprot;acc:p78426]	Subtracted		Low confidence	64485.5	70068.3	5582.8
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Divided	Rooted	High confidence	55.65	65.1448	1.17062
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]		Measured		23693.7	18263	1.29736
	myosin xv (unconventional myosin-15). [swissprot;acc:q9ukn7]	Subtracted			4489.19	2765.82	1723.37
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]		Rooted	Low confidence	70.7428	75.3259	4.5831
	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [swissprot;acc:q9byz6]	Divided	Ranked		212.695	201.131	1.05749
			Rooted		68.0417	72.5283	1.06594
		Subtracted	Ranked		212.695	201.131	11.564
	vacuolar assembly protein vps41 homolog (s53). [swissprot;acc:p49754]		Measured		7497.17	8131.56	634.39
168	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]		Squared	High confidence	69165.6	52992.1	16173.5
	beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121]	Divided	Rooted	Low confidence	72.4531	77.213	1.0657
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Subtracted	Ranked	High confidence	312	284	28
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Divided			82.5916	98.0548	1.18722
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]	Subtracted	Measured		4489.19	2765.82	1723.37
	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]	Divided		Low confidence	12376.4	11436.5	1.08218
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]			High confidence	23693.7	18263	1.29736

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.