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

Results: HTML CSV LaTeX

Showing element 5430 to 5479 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
2715	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Divided	5332.98	5351.72	1.00351
2716	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]
	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	Subtracted	5603.24	5583.64	19.6
2717	palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [swissprot;acc:p50897]	Divided			1.00351
	syntaxin 1b. [swissprot;acc:q15531]	Subtracted			19.6
2718	beta-soluble nsf attachment protein (snap-beta) (n-ethylmaleimide- sensitive factor attachment protein, beta). [swissprot;acc:q9h115]	Divided			1.00351
	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	Subtracted			19.6
2719	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
	syntaxin 16 (syn16). [swissprot;acc:o14662]	Divided			1.00351
2720	27 kda golgi snare protein (golgi snap receptor complex member 2) (membrin). [swissprot;acc:o14653]
	cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574]	Subtracted	3953.53	3972.32	18.79
2721	oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]	Divided	5603.24	5583.64	1.00351
2722	alpha-soluble nsf attachment protein (snap-alpha) (n-ethylmaleimide- sensitive factor attachment protein, alpha). [swissprot;acc:p54920]
	senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]	Subtracted	3953.53	3972.32	18.79
2723	adipocyte plasma membrane-associated protein (bscv protein). [swissprot;acc:q9hdc9]	Divided	5603.24	5583.64	1.00351
	oligophrenin 1. [swissprot;acc:o60890]	Subtracted	3953.53	3972.32	18.79
2724	n-acetyllactosaminide beta-1,3-n-acetylglucosaminyltransferase (ec 2.4.1.149) (poly-n-acetyllactosamine extension enzyme) (i-beta- 1,3-n-acetylglucosaminyltransferase) (ignt) (udp-glcnac:betagal beta- 1,3-n-acetylglucosaminyltransferase 6). [swissprot;acc:o43505]		5332.98	5351.72	18.74
	synaptosomal-associated protein 29 (snap-29) (vesicle-membrane fusion protein snap-29) (soluble 29 kda nsf attachment protein). [swissprot;acc:o95721]	Divided	5603.24	5583.64	1.00351
2725	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Subtracted	5332.98	5351.72	18.74
	syntaxin 1b. [swissprot;acc:q15531]	Divided	5603.24	5583.64	1.00351
2726	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]		5332.98	5351.72
	mitochondrial import inner membrane translocase subunit tim10. [swissprot;acc:q9y5j8]	Subtracted			18.74
2727	fumarate hydratase, mitochondrial precursor (ec 4.2.1.2) (fumarase). [swissprot;acc:p07954]
	melanoma antigen p15 (melanoma-associated antigen recognized by t lymphocytes). [swissprot;acc:q13084]	Divided	5603.24	5583.64	1.00351
2728	dna-binding protein rfxank (regulatory factor x subunit b) (rfx-b) (ankyrin repeat family a protein 1). [swissprot;acc:o14593]
	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	Subtracted	5333	5351.61	18.61
2729	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]		4113.79	4095.53	18.26
	probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	Divided	5333	5351.61	1.00349
2730	myelin gene expression factor 2. [refseq;acc:nm_016132]		5214.9	5197.18	1.00341
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Subtracted	4113.79	4095.53	18.26
2731	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]
	transcription factor p65 (nuclear factor nf-kappa-b p65 subunit). [swissprot;acc:q04206]	Divided	7913.63	7939.94	1.00332
2732	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]	Subtracted	4113.79	4095.53	18.26
	transcription factor relb (i-rel). [swissprot;acc:q01201]	Divided	7913.63	7939.94	1.00332
2733	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	Subtracted	4113.79	4095.53	18.26
	nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [swissprot;acc:p25963]	Divided	7913.63	7939.94	1.00332
2734	60s ribosomal protein l18. [swissprot;acc:q07020]	Subtracted	4113.79	4095.53	18.26
	coproporphyrinogen iii oxidase, mitochondrial precursor (ec 1.3.3.3) (coproporphyrinogenase) (coprogen oxidase) (cox). [swissprot;acc:p36551]	Divided	7913.63	7939.94	1.00332
2735	creatine kinase, b chain (ec 2.7.3.2) (b-ck). [swissprot;acc:p12277]		8991.87	9019.99	1.00313
	myelin gene expression factor 2. [refseq;acc:nm_016132]	Subtracted	5214.9	5197.18	17.72
2736	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	Divided	4887.59	4902.08	1.00296
	trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169]	Subtracted	4163.36	4145.95	17.41
2737	protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316]		4137.61	4152.72	15.11
	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]	Divided	4486.83	4499.52	1.00283
2738	inhibitor of growth family, member 1; inhibitor of growth 1. [refseq;acc:nm_005537]	Subtracted	4887.59	4902.08	14.49
	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	Divided	4486.83	4499.52	1.00283
2739	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]		4877.74	4890.64	1.00264
		Subtracted			12.9
2740	dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434]	Divided	4200.59	4210.94	1.00246

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.