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

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Showing element 3180 to 3229 of 77072 in total

Rank	Network Comparison Type	Value Type	Interaction Map	description	green	red	Filtered	network_comparison
100	Divided	Squared	Low confidence	tumor protein p53 inducible protein 3; quinone oxidoreductase homolog; p53-induced gene 3 protein. [refseq;acc:nm_004881]	82296.2	70019.5	1	1.17533
		Rooted	High confidence	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	15.3244	20.0501	0	1.30838
				regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	36.9304	47.6504	1	1.29028
			Low confidence	natural resistance-associated macrophage protein 1 (nramp 1). [swissprot;acc:p49279]	69.4515	63.7749		1.08901
				transcription initiation factor iie, beta subunit (tfiie-beta). [swissprot;acc:p29084]	7.07107	5.47723	0	1.29099
	Subtracted	Measured	High confidence	dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9]	3010.22	2698.62		311.6
				septin 6. [swissprot;acc:q14141]	18957.1	15959.9	1	2997.2
			Low confidence	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	11435.8	12375.5		939.7
				zinc finger protein 117 (zinc finger protein hpf9) (fragment). [swissprot;acc:q03924]	1969.43	2352.42	0	382.99
		Ranked	High confidence	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	10470.6	12584.5		2113.9
				fos-related antigen 2. [swissprot;acc:p15408]	161.046	204.641	1	43.595
			Low confidence	b(0,+)-type amino acid transporter 1 (b(0,+)at) (glycoprotein- associated amino acid transporter b0,+at1). [swissprot;acc:p82251]	185.679	200.497		14.818
				putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	13865.5	11725.7	0	2139.8
		Squared	High confidence	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	311745	310373		1372
				septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	125229	89182.8	1	36046.2
			Low confidence	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	13564.1	16325.5	0	2761.4
				monocarboxylate transporter 8 (mct 8) (x-linked pest-containing transporter) (mct 7). [swissprot;acc:p36021]	72791.6	63904	1	8887.6
		Rooted	High confidence	ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	17.665	22.4608	0	4.7958
				tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616]	35.798	19.9625	1	15.8355
			Low confidence	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	68.2337	61.9982		6.2355
				zinc finger protein 84 (zinc finger protein hpf2). [swissprot;acc:p51523]	40.7113	45.3043	0	4.593
101	Divided	Measured	High confidence	cullin homolog 2 (cul-2). [swissprot;acc:q13617]	3225.65	2353.63	1	1.3705
				putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7]	977	1442	0	1.47595
			Low confidence	60s ribosomal protein l37a. [swissprot;acc:p12751]	362.955	535.61		1.47569
				set and mynd domain containing protein 1. [sptrembl;acc:q8nb12]	6330.03	5752.65	1	1.10037
		Ranked	High confidence	dj947l8.1.1 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4v7]	11915.2	14548.5	0	1.221
				melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	110.265	88.2482	1	1.24949
			Low confidence	leucine zipper domain protein. [refseq;acc:nm_024589]	238.82	221.996		1.07579
				similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	10598.3	8703.84	0	1.21766
		Squared	High confidence	cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	143584	222655	1	1.5507
				transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664]	441.285	956.375	0	2.16725
			Low confidence	b24o18.3 (pom121 membrane glycoprotein (rat homolog)-like 2). [sptrembl;acc:q96kw2]	12.7302	27.0961		2.12849
				raptor; p150 target of rapamycin (tor)-scaffold protein containing wd-repeats. [refseq;acc:nm_020761]	54384.3	63526.9	1	1.16811
		Rooted	High confidence	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]	36.9304	47.6504		1.29028
				low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	9.74679	12.6886	0	1.30182
			Low confidence	dj947l8.1.6 (novel cub and sushi (scr repeat) domain protein) (fragment). [sptrembl;acc:q9h4w2]	17.6786	13.7191		1.28861
				vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]	75.3346	69.1897	1	1.08881
	Subtracted	Measured	High confidence	formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892]	330.189	638.862	0	308.673
				septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	17655.2	14924.4	1	2730.8
			Low confidence	pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999]	11612.9	10685.5		927.4
				zinc finger protein 141. [swissprot;acc:q15928]	1969.43	2352.42	0	382.99
		Ranked	High confidence	coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606]	14662.1	12577.8		2084.3
				protein fosb (g0/g1 switch regulatory protein 3). [swissprot;acc:p53539]	161.051	204.641	1	43.59
			Low confidence	coagulation factor xiii a chain precursor (ec 2.3.2.13) (protein- glutamine gamma-glutamyltransferase a chain) (transglutaminase a chain). [swissprot;acc:p00488]	211.713	226.395		14.682
				kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	10030.4	7923.89	0	2106.51
		Squared	High confidence	ethanolamine-phosphate cytidylyltransferase (ec 2.7.7.14) (phosphorylethanolamine transferase) (ctp:phosphoethanolamine cytidylyltransferase). [swissprot;acc:q99447]	3966.41	5294.83		1328.42
				septin 6. [swissprot;acc:q14141]	124854	88953.6	1	35900.4
			Low confidence	solute carrier family 16 (monocarboxylic acid transporters), member 10; t-type amino acid transporter 1. [refseq;acc:nm_018593]	72790.2	63903.1		8887.1
				splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	11941.1	9225.25	0	2715.85
		Rooted	High confidence	dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552]	35.798	19.9625	1	15.8355

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.