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

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Showing element 2725 to 2774 of 12912 in total

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

Rank	Hugo	description	red	green	network_comparison
2725	STX1B	syntaxin 1b. [swissprot;acc:q15531]	5603.24	5583.64	1.00351
2726	FH	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]	5332.98	5351.72
2727	MRPL28	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	5603.24	5583.64
2728	RFXANK	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
2729	NUAK1	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	5333	5351.61	1.00349
2730	MYEF2	myelin gene expression factor 2. [refseq;acc:nm_016132]	5214.9	5197.18	1.00341
2731	RELA	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	7913.63	7939.94	1.00332
2732	RELB	transcription factor relb (i-rel). [swissprot;acc:q01201]
2733	NFKBIA	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]
2734	CPOX	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
2735	CKB	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]	8991.87	9019.99	1.00313
2736	ING1	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	4887.59	4902.08	1.00296
2737	no value	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	4486.83	4499.52	1.00283
2738	GTF2H1	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]
2739	ING2	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]	4877.74	4890.64	1.00264
2740	POLR2H	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	4200.59	4210.94	1.00246
2741	SNX5	sorting nexin 5. [swissprot;acc:q9y5x3]	5339.67	5327.2	1.00234
2742	SLC15A1	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	10198.1	10174.3
2743	RPLP2	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	4824.49	4813.92	1.0022
2744	SLC15A2	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	10143.6	10163.6	1.00197
2745	TRIM3	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	7746.61	7757.23	1.00137
2746	no value	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	4188.5	4194.22
2747	PNO1	putatative 28 kda protein. [refseq;acc:nm_020143]	4708.68	4702.58	1.0013
2748	STX6	syntaxin 6. [swissprot;acc:o43752]	5296.39	5301.11	1.00089
2749	ZFHX3	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911]	7776.91	7783.48	1.00084
2750	STX10	syntaxin 10 (syn10). [swissprot;acc:o60499]	5294.28	5298.42	1.00078
2751	TRIM2	tripartite motif protein 2. [swissprot;acc:q9c040]	7810.47	7812.55	1.00027
2752	SETMAR	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	4521.42	4521.87	1.0001
2753	CLEC4M	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]
2754	FCER2	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
2755	CD209	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]
2756	no value	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	0.00001	0.00001	1
2757	NAP1L1	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
2758	NAP1L2	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
2759	RXRA	retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
2760	TAL2	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
2761	GNB1L	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]
2762	DRG1	developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295]
2763	PCGF3	ring finger protein 3. [refseq;acc:nm_006315]
2764	RAB11B	ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]
2765	no value	histone h2a.e (h2a/e). [swissprot;acc:q99878]
2766	SS18L1	ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]
2767	no value	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
2768	HIST2H2AB	histone h2a.x (h2a/x). [swissprot;acc:p16104]
2769	HIST2H2AC	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]
2770	NIPSNAP1	nipsnap1 protein. [swissprot;acc:q9bpw8]
2771	TBX1	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]
2772	NUDT14	uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]
2773	BMP8A	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
2774	C3orf37	dc12 protein. [refseq;acc:nm_020187]

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.