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

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Showing element 1362 to 1411 of 12912 in total

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

Rank	Value Type	description	red	green	network_comparison
341	Ranked	60s ribosomal protein l9. [swissprot;acc:p32969]	240.243	263.798	1.09805
	Squared	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	32056.4	39965.8	1.24673
	Rooted	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	51.9812	57.5858	1.10782
342	Measured	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	20446.1	24136.4	1.18049
	Ranked	40s ribosomal protein s20. [swissprot;acc:p17075]	243.5	267.21	1.09737
	Squared	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	70830.5	56822	1.24653
	Rooted	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	49.2715	54.5757	1.10765
343	Measured	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	20446.1	24136.4	1.18049
	Ranked	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	241.625	265.136	1.0973
	Squared	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]	70830.5	56822	1.24653
	Rooted	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	50.3169	45.4333	1.10749
344	Measured	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	20446.1	24136.4	1.18049
	Ranked	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	241.625	265.136	1.0973
	Squared	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	37226.9	46400.1	1.24641
	Rooted	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	49.4233	54.7327	1.10743
345	Measured	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	20446.1	24136.4	1.18049
	Ranked	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	242.14	265.697	1.09729
	Squared	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	35793	44595.3	1.24592
	Rooted	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	56.2615	62.2958	1.10725
346	Measured	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	14229.2	16780.7	1.17931
	Ranked	40s ribosomal protein s3. [swissprot;acc:p23396]	241.612	265.119	1.09729
	Squared	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060]	34018.3	42373	1.24559
	Rooted	grb2-related adaptor protein. [swissprot;acc:q13588]	61.4282	68.0107	1.10716
347	Measured	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	4991.02	5885.09	1.17914
	Ranked	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	242.14	265.697	1.09729
	Squared	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	16573.6	20637.8	1.24522
	Rooted	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	66.4284	60.0004	1.10713
348	Measured	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]	4991.02	5885.09	1.17914
	Ranked	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	242.14	265.696	1.09728
	Squared	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530]	42566.2	52985.3	1.24477
	Rooted	ad24 protein. [refseq;acc:nm_022451]	49.2558	54.5235	1.10695
349	Measured	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	4714.85	5554.38	1.17806
	Ranked	surfeit locus protein 5. [swissprot;acc:q15528]	242.14	265.696	1.09728
	Squared	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [swissprot;acc:q99962]	35533.9	44227	1.24464
	Rooted	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [swissprot;acc:q9y4z0]	56.0061	61.9704	1.10649
350	Measured	sedlin. [swissprot;acc:o14582]	17396.9	20483.9	1.17745
	Ranked	zinc finger protein 291. [swissprot;acc:q9by12]	242.14	265.696	1.09728
	Squared	armet protein precursor (arginine-rich protein). [swissprot;acc:p55145]	35508.7	44191.4	1.24452
	Rooted	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [refseq;acc:nm_145117]	61.3383	67.8668	1.10643
351	Measured	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]	17396.9	20483.9	1.17745
	Ranked	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	242.14	265.696	1.09728
	Squared	histidine decarboxylase (ec 4.1.1.22) (hdc). [swissprot;acc:p19113]	35508.6	44191.3	1.24452
	Rooted	e2a-pbx1-associated protein; putative 47 kda protein. [refseq;acc:nm_020140]	61.3352	67.8618	1.10641
352	Measured	bet3 homolog. [swissprot;acc:o43617]	17396.9	20483.9	1.17745
	Ranked	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]	242.14	265.696	1.09728
	Squared	40s ribosomal protein s28. [swissprot;acc:p25112]	30682.9	38183.6	1.24446
	Rooted	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [refseq;acc:nm_020443]	61.3354	67.8621	1.10641
353	Measured	p66 alpha. [refseq;acc:nm_017660]	12839	10911.1	1.17669
	Ranked	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	231.73	211.252	1.09694
	Squared	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [swissprot;acc:q15233]	71383	57399.3	1.24362

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.