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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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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 3986 to 4035 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
997	lysophospholipase i; lysophospholipase 1; lysophospholipid-specific lysophospholipase; acyl-protein thioesterase-1. [refseq;acc:nm_006330]	Squared	25141.4	28896.8	1.14937
	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]	Ranked	219.656	212.547	1.03345
	nucleolar protein family a, member 2; component of the h/aca snornp. [refseq;acc:nm_017838]	Measured	5144.74	5634	1.0951
998	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]	Ranked	225.557	218.271	1.03338
	mawd binding protein (unknown protein 32 from 2d-page of liver tissue). [swissprot;acc:p30039]	Squared	25141.4	28896.8	1.14937
	transcription initiation factor iif, alpha subunit (tfiif-alpha) (transcription initiation factor rap74). [swissprot;acc:p35269]	Measured	5144.74	5634	1.0951
	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822]	Rooted	69.5394	73.3277	1.05448
999	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
	lysophospholipase ii; acyl-protein thioesterase. [refseq;acc:nm_007260]	Squared	25141.4	28896.8	1.14937
	triacylglycerol lipase, gastric precursor (ec 3.1.1.3) (gastric lipase) (gl). [swissprot;acc:p07098]	Measured	5680.76	6220.45	1.095
	vinculin (metavinculin). [swissprot;acc:p18206]	Ranked	215.92	208.95	1.03336
1000	ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]	Measured	5680.76	6220.45	1.095
	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	Squared	27225.4	31287.9	1.14922
	kinesin protein. [refseq;acc:nm_032559]	Rooted	59.2757	62.5044	1.05447
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Ranked	225.167	217.922	1.03325
1001	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	Rooted	67.7551	71.4422	1.05442
	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073]	Squared	21068.2	24205.2	1.1489
	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571]	Measured	5680.76	6220.45	1.095
	sprouty homolog 3 (spry-3). [swissprot;acc:o43610]	Ranked	225.167	217.922	1.03325
1002	40s ribosomal protein s30. [swissprot;acc:q05472]	Rooted	61.3513	64.6874	1.05438
	seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]	Measured	5680.76	6220.45	1.095
	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]	Squared	21068.2	24205.2	1.1489
	sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609]	Ranked	225.167	217.922	1.03325
1003	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]	Squared	17541.4	20148.6	1.14863
	ny-ren-62 antigen (fragment). [sptrembl;acc:q9y590]	Rooted	59.2915	62.5118	1.05431
	seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]	Measured	5680.76	6220.45	1.095
	sprouty homolog 2 (spry-2). [swissprot;acc:o43597]	Ranked	225.167	217.922	1.03325
1004	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	Squared	17541.4	20148.6	1.14863
	interleukin enhancer-binding factor 1 (cellular transcription factor ilf-1). [swissprot;acc:q01167]	Rooted	61.5654	64.9046	1.05424
	o-sialoglycoprotein endopeptidase. [refseq;acc:nm_017807]	Measured	5391.64	5903.72	1.09498
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Ranked	238.725	231.059	1.03318
1005	annexin a7 (annexin vii) (synexin). [swissprot;acc:p20073]	Measured	5780.34	6329.3	1.09497
	dynein intermediate chain 1, cytosolic (dh ic-1) (cytoplasmic dynein intermediate chain 1). [swissprot;acc:o14576]	Ranked	225.448	218.232	1.03307
	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]	Squared	17541.4	20148.6	1.14863
	xenotropic and polytropic retrovirus receptor. [refseq;acc:nm_004736]	Rooted	64.9107	68.4287	1.0542
1006	cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	Ranked	116.524	120.375	1.03305
	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]	Squared	17541.4	20148.6	1.14863
	kinesin-like protein kif2 (kinesin-2) (hk2). [swissprot;acc:o00139]	Rooted	59.3039	62.5177	1.05419
	peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936]	Measured	5707.73	6249.1	1.09485
1007	eukaryotic translation initiation factor 4e (eif-4e) (eif4e) (mrna cap-binding protein) (eif-4f 25 kda subunit). [swissprot;acc:p06730]	Squared	17603.1	20218.5	1.14858
	hypoxia-inducible factor-3 alpha isoform a; inhibitory pas domain protein. [refseq;acc:nm_152794]	Measured	5707.73	6249.1	1.09485
	pinin, desmosome associated protein; pinin. [refseq;acc:nm_002687]	Rooted	64.0132	67.4724	1.05404
	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	Ranked	162.055	156.884	1.03296
1008	bai1-associated protein 3; bai-associated protein 3. [refseq;acc:nm_003933]	Squared	17603.1	20218.5	1.14858
	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]	Rooted	51.2693	54.0336	1.05392
	single-minded homolog 1. [swissprot;acc:p81133]	Measured	5707.73	6249.1	1.09485
	wd-repeat protein bing4. [swissprot;acc:o15213]	Ranked	243.227	235.475	1.03292
1009	40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	Squared	21492.5	24677.4	1.14819
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Ranked	229.116	221.823	1.03288
	exportin 1; exportin-1 (required for chromosome region maintenance); exportin 1 (crm1, yeast, homolog); crm1, yeast, homolog. [refseq;acc:nm_003400]	Rooted	58.8768	62.0483	1.05387

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.