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 6908 to 6957 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
432	mct-1 protein. [refseq;acc:nm_014060]	Ranked	Subtracted	1	226.313	243.03	16.717
	mitochondrial processing peptidase beta subunit, mitochondrial precursor (ec 3.4.24.64) (beta-mpp) (p-52). [swissprot;acc:o75439]	Measured	Divided		5244.71	6036.27	1.15093
	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]		Subtracted		6739.81	7644.62	904.81
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Rooted		0	11.9476	12.4394	0.4918
	signal-induced proliferation-associated 1-like 1. [refseq;acc:nm_015556]		Divided		12.5074	12.1701	1.02772
433	bystin. [swissprot;acc:q13895]		Subtracted		29.2217	28.7356	0.4861
	cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]	Squared		1	26598.9	32283.5	5684.6
	dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9]			0	2.36686	4.90793	2.54107
	gamma-aminobutyric-acid receptor gamma-1 subunit precursor (gaba(a) receptor). [swissprot;acc:q8n1c3]	Measured		1	6739.82	7644.62	904.8
	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]	Rooted			66.082	71.6526	5.5706
	grancalcin. [swissprot;acc:p28676]	Squared	Divided		29095.7	35338.3	1.21455
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 like subunit. [swissprot;acc:q9y3k8]	Measured	Subtracted	0	377.445	359.98	17.465
	h2a histone family, member j isoform 1. [refseq;acc:nm_018267]	Ranked			21205	20914	291
	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	Rooted	Divided	1	54.4927	49.6125	1.09837
	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713]	Measured			5244.88	6036.38	1.15091
	mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]	Ranked	Subtracted		226.313	243.03	16.717
	my016 protein. [sptrembl;acc:q9h3k6]	Squared	Divided	0	1279.28	1234.42	1.03634
	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]	Ranked		1	212.547	229.411	1.07934
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	Rooted		0	13.7373	13.373	1.02724
	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	Measured			100.5	103.25	1.02736
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Ranked			772	754	1.02387
434	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]	Measured	Subtracted		2281.12	2263.85	17.27
	ad24 protein. [refseq;acc:nm_022451]	Ranked		1	251.334	234.672	16.662
	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Rooted	Divided	0	14.6265	15.0206	1.02694
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]		Subtracted		55.5596	55.0873	0.4723
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Ranked	Divided		10028.5	10261.5	1.02323
	gamma-aminobutyric-acid receptor alpha-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p47869]	Measured	Subtracted	1	6739.83	7644.63	904.8
	interleukin-1 receptor-associated kinase 4; interleukin-1 receptor associated kinase 4. [refseq;acc:nm_016123]	Rooted			66.082	71.6526	5.5706
	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]	Squared			26598.9	32283.5	5684.6
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Ranked		0	12532.2	12808.8	276.6
	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	Squared			8.27667	5.86733	2.40934
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]		Divided	1	18306.1	22230.6	1.21438
	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	Ranked			212.547	229.411	1.07934
	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	Measured		0	201	206.5	1.02736
	thymic stromal co-transporter. [refseq;acc:nm_033051]	Rooted		1	54.4927	49.6125	1.09837
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Measured			5246.38	6037.37	1.15077
	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	Squared		0	3778.25	3909.18	1.03465
435	60s ribosomal protein l19. [swissprot;acc:p14118]	Rooted		1	50.832	46.3081	1.09769
	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	Measured	Subtracted	0	2319.24	2335.98	16.74
	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Ranked			14010.2	13737.2	273
	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	Squared	Divided	1	26598.9	32283.5	1.21372
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Measured		0	5891.28	5737.71	1.02677
	enigma protein; lim domain protein. [refseq;acc:nm_005451]	Squared	Subtracted		21.836	19.5177	2.3183
	gamma-aminobutyric-acid receptor gamma-2 subunit precursor (gaba(a) receptor). [swissprot;acc:p18507]	Measured		1	6739.82	7644.62	904.8
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Ranked	Divided	0	8770.94	8574.04	1.02296
	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	Rooted			14.6265	15.0206	1.02694
	phosphatidylserine receptor; phosphatidylserine receptor beta. [refseq;acc:nm_015167]		Subtracted	1	66.082	71.6526	5.5706
	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Ranked	Divided		221.522	205.286	1.07909
	proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903]	Measured			5233.86	6022.6	1.1507
	seven in absentia homolog 1. [refseq;acc:nm_003031]	Rooted	Subtracted	0	28.462	28.9328	0.4708

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.