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

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Showing element 6208 to 6257 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
1552	zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312]	Squared	27018.7	30041.5	1.11188
1553	adenosylhomocysteinase (ec 3.3.1.1) (s-adenosyl-l-homocysteine hydrolase) (adohcyase). [swissprot;acc:p23526]	Ranked	215.389	211.833	1.01679
	alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588]	Rooted	54.3745	52.4728	1.03624
	elongation factor 1-alpha 2 (ef-1-alpha-2) (elongation factor 1 a-2) (eef1a-2) (statin s1). [swissprot;acc:q05639]	Squared	27018.7	30041.5	1.11188
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Measured	5875.75	6302.76	1.07267
1554	26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	Squared	26642.1	29622.1	1.11185
	acyl-coa dehydrogenase, short/branched chain specific, mitochondrial precursor (ec 1.3.99.-) (sbcad) (2-methyl branched chain acyl-coa dehydrogenase) (2-mebcad) (2-methylbutyryl-coenzyme a dehydrogenase) (2-methylbutyryl-coa dehydrogenase). [swissprot;acc:p45954]	Rooted	63.9658	66.2831	1.03623
	c-terminal binding protein 1 (ctbp1). [swissprot;acc:q13363]	Ranked	196.215	193.018	1.01656
	prefoldin subunit 1. [swissprot;acc:o60925]	Measured	5875.75	6302.76	1.07267
1555	pas domain containing serine/threonine kinase; pas-serine/threonine kinase. [refseq;acc:nm_015148]	Ranked	196.192	192.996	1.01656
	secreted modular calcium-binding protein 2; smooth muscle associated protein 2. [refseq;acc:nm_022138]	Measured	5875.75	6302.76	1.07267
	target of myb protein 1. [swissprot;acc:o60784]	Squared	24710	27473.8	1.11185
	vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269]	Rooted	63.4077	65.7034	1.03621
1556	b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	Ranked	196.192	192.996	1.01656
	choline dehydrogenase. [refseq;acc:nm_018397]	Measured	5875.75	6302.76	1.07267
	huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229]	Squared	24712.8	27476.2	1.11182
	kccr13l. [refseq;acc:nm_139179]	Rooted	61.0148	63.2233	1.0362
1557	dna repair protein rad51 homolog 1 (hrad51) (hsrad51). [swissprot;acc:q06609]
	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	Squared	24712.9	27476.3	1.11182
	vacuolar protein sorting 18 (hvps18). [swissprot;acc:q9p253]	Measured	6018.7	6455.7	1.07261
	zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623]	Ranked	196.192	192.996	1.01656
1558	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]		196.171	192.977	1.01655
	rad54-like protein; rad54 homolog. [refseq;acc:nm_003579]	Rooted	61.6942	63.9187	1.03606
	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	Squared	24716.5	27479.3	1.11178
	vacuolar protein sorting 33b (hvps33b). [swissprot;acc:q9h267]	Measured	6048.57	6487.65	1.07259
1559	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	Ranked	196.191	192.996	1.01655
	eyes absent homolog 3. [swissprot;acc:q99504]	Rooted	61.9436	64.1746	1.03602
	tensin. [refseq;acc:nm_022648]	Squared	27803.3	30910.9	1.11177
	vacuolar protein sorting 11 (hvps11) (pp3476). [swissprot;acc:q9h270]	Measured	6048.57	6487.65	1.07259
1560	ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	Squared	26174.3	29098.4	1.11172
	colorectal mutant cancer protein (mcc protein). [swissprot;acc:p23508]	Rooted	66.302	68.6843	1.03593
	p66 alpha. [refseq;acc:nm_017660]	Ranked	167.687	170.455	1.01651
	vacuolar protein sorting 33a (hvps33a). [swissprot;acc:q96ax1]	Measured	6048.57	6487.65	1.07259
1561	40s ribosomal protein s7 (s8). [swissprot;acc:p23821]	Squared	26174.3	29098.4	1.11172
	mitotic spindle assembly checkpoint protein mad2a (mad2-like 1) (hsmad2). [swissprot;acc:q13257]	Rooted	65.8508	68.2155	1.03591
	transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]	Ranked	167.687	170.455	1.01651
	vacuolar protein sorting 16 (hvps16). [swissprot;acc:q9h269]	Measured	6078.43	6519.6	1.07258
1562	26s proteasome-associated pad1 homolog. [refseq;acc:nm_005805]	Squared	26174.3	29098.4	1.11172
	adenylyl cyclase-associated protein 2 (cap 2). [swissprot;acc:p40123]	Measured	5984.88	6419.11	1.07255
	probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11]	Rooted	65.8508	68.2155	1.03591
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	Ranked	167.687	170.455	1.01651
1563	apolipoprotein b-100 precursor (apo b-100) [contains: apolipoprotein b-48 (apo b-48)]. [swissprot;acc:p04114]	Squared	26174.3	29098.4	1.11172
	atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542]	Ranked	218.277	214.739	1.01648
	proteasome subunit beta type 6 precursor (ec 3.4.25.1) (proteasome delta chain) (macropain delta chain) (multicatalytic endopeptidase complex delta chain) (proteasome subunit y). [swissprot;acc:p28072]	Measured	6221.35	6672.51	1.07252
	upstream stimulatory factor 1 (major late transcription factor 1). [swissprot;acc:p22415]	Rooted	64.5089	66.8255	1.03591
1564	atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]	Ranked	218.277	214.739	1.01648
	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	Squared	31878.5	35436.9	1.11162
	proteasome subunit beta type 9 precursor (ec 3.4.25.1) (proteasome chain 7) (macropain chain 7) (multicatalytic endopeptidase complex chain 7) (ring12 protein) (low molecular mass protein 2). [swissprot;acc:p28065]	Measured	6257.62	6711.4	1.07252
	tata box binding protein (transcription initiation factor tfiid) (tata-box factor) (tata sequence-binding protein) (tbp). [swissprot;acc:p20226]	Rooted	65.8508	68.2155	1.03591
1565	eukaryotic translation initiation factor 3 subunit 11 (eif-3 p25) (eif3k) (muscle specific gene m9 protein) (ptd001) (hspc029) (arg134). [swissprot;acc:q9ubq5]	Ranked	221.128	224.767	1.01646

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.