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

Results: HTML CSV LaTeX

Showing element 2730 to 2779 of 6456 in total

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

Rank	description	red	network_comparison	green
2730	myelin gene expression factor 2. [refseq;acc:nm_016132]	5214.9	1.00341	5197.18
2731	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	7913.63	1.00332	7939.94
2732	transcription factor relb (i-rel). [swissprot;acc:q01201]
2733	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]
2734	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]
2735	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]	8991.87	1.00313	9019.99
2736	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	4887.59	1.00296	4902.08
2737	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	1.00283	4499.52
2738	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	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]	4877.74	1.00264	4890.64
2740	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	1.00246	4210.94
2741	sorting nexin 5. [swissprot;acc:q9y5x3]	5339.67	1.00234	5327.2
2742	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	60s acidic ribosomal protein p2. [swissprot;acc:p05387]	4824.49	1.0022	4813.92
2744	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	10143.6	1.00197	10163.6
2745	tripartite motif protein 3 (ring finger protein 22) (brain-expressed ring finger protein). [swissprot;acc:o75382]	7746.61	1.00137	7757.23
2746	hpaii tiny fragments locus 9c. [refseq;acc:nm_022727]	4188.5		4194.22
2747	putatative 28 kda protein. [refseq;acc:nm_020143]	4708.68	1.0013	4702.58
2748	syntaxin 6. [swissprot;acc:o43752]	5296.39	1.00089	5301.11
2749	alpha-fetoprotein enhancer binding protein (at motif-binding factor) (at-binding transcription factor 1). [swissprot;acc:q15911]	7776.91	1.00084	7783.48
2750	syntaxin 10 (syn10). [swissprot;acc:o60499]	5294.28	1.00078	5298.42
2751	tripartite motif protein 2. [swissprot;acc:q9c040]	7810.47	1.00027	7812.55
2752	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	4521.42	1.0001	4521.87
2753	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]
2754	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]
2755	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]
2756	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	0.00001	1	0.00001
2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
2759	retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
2761	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	developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295]
2763	ring finger protein 3. [refseq;acc:nm_006315]
2764	ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]
2765	histone h2a.e (h2a/e). [swissprot;acc:q99878]
2766	ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]
2767	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	histone h2a.x (h2a/x). [swissprot;acc:p16104]
2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]
2770	nipsnap1 protein. [swissprot;acc:q9bpw8]
2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]
2772	uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]
2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
2774	dc12 protein. [refseq;acc:nm_020187]
2775	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]
2776	bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745]
2777	guanine nucleotide exchange factor mss4 (rab interacting factor). [swissprot;acc:p47224]
2778	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [sptrembl;acc:q8nhw3]
2779	caveolin-3 (m-caveolin). [swissprot;acc:p56539]

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.