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

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Showing element 3632 to 3681 of 19268 in total

Value Type  : Ranked

Rank	description	Filtered	Network Comparison Type	Interaction Map	red	green	network_comparison
454	zinc finger protein 7 (zinc finger protein kox4) (zinc finger protein hf.16). [swissprot;acc:p17097]	0	Subtracted	Low confidence	4253.91	4850.65	596.74
455	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	1		High confidence	224.161	207.972	16.189
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	0			12189.6	12378.3	188.7
	dynein heavy chain, cytosolic (dyhc) (cytoplasmic dynein heavy chain 1) (dhc1) (fragment). [swissprot;acc:q14204]		Divided	Low confidence	10373.7	9689.7	1.07059
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	1	Subtracted		207.812	200.994	6.818
	mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584]		Divided	High confidence	210.225	226.578	1.07779
	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]	0			13933.5	14204.8	1.01947
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	1		Low confidence	210.251	203.241	1.03449
	zinc finger protein 304. [swissprot;acc:q9hcx3]	0	Subtracted		4253.74	4850.47	596.73
456	atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]	1	Divided	High confidence	210.225	226.578	1.07779
	f23269_2. [sptrembl;acc:o75290]	0	Subtracted	Low confidence	4253.5	4850.22	596.72
	glycerol kinase, testis specific 2 (ec 2.7.1.30) (atp:glycerol 3- phosphotransferase) (glycerokinase) (gk). [swissprot;acc:q14410]		Divided		13559	14512.9	1.07035
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	1	Subtracted		207.812	200.994	6.818
	histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351]	0		High confidence	7965.06	7790.78	174.28
	u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661]	1			224.161	207.972	16.189
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]		Divided	Low confidence	210.251	203.241	1.03449
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	0		High confidence	16416.1	16721.6	1.01861
457	ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	1	Subtracted		210.578	226.764	16.186
	calcyphosine. [swissprot;acc:q13938]	0	Divided	Low confidence	10007.1	9350.72	1.0702
	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]		Subtracted	High confidence	7965.06	7790.78	174.28
	dj153g14.3 (novel c2h2 type zinc finger protein) (fragment). [sptrembl;acc:q9ujn7]			Low confidence	4253.5	4850.22	596.72
	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	1			207.812	200.994	6.818
	ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927]		Divided	High confidence	210.225	226.578	1.07779
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]			Low confidence	210.251	203.241	1.03449
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	0		High confidence	16416.1	16721.6	1.01861
458	adapter-related protein complex 1 beta 1 subunit (beta-adaptin 1) (adaptor protein complex ap-1 beta-1 subunit) (golgi adaptor ha1/ap1 adaptin beta subunit) (clathrin assembly protein complex 1 beta large chain). [swissprot;acc:q10567]	1		Low confidence	206.948	200.058	1.03444
	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]		Subtracted	High confidence	251.653	235.506	16.147
	dj18d14.4 (cytochrome p450, subfamily iva, polypeptide 11). [sptrembl;acc:q9ntl5]			Low confidence	203.074	196.277	6.797
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	0		High confidence	7759.36	7586.42	172.94
	presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]		Divided	Low confidence	13390	14326	1.0699
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	1		High confidence	235.922	218.925	1.07764
	williams beuren syndrome chromosome region 20c isoform 1. [refseq;acc:nm_032158]	0			16416.1	16721.6	1.01861
	zinc finger protein 415. [refseq;acc:nm_018355]		Subtracted	Low confidence	4253.34	4850.04	596.7
459	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	1	Divided	High confidence	233.529	216.737	1.07748
	cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]	0	Subtracted		5905	6073	168
	cytochrome p450 4a11 precursor (ec 1.14.15.3) (cypiva11) (fatty acid omega-hydroxylase) (p-450 hk omega) (lauric acid omega-hydroxylase) (cyp4aii) (p450-hl-omega). [swissprot;acc:q02928]	1		Low confidence	203.077	196.283	6.794
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]		Divided		207.797	214.954	1.03444
	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]	0			9431	8815	1.06988
	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	1	Subtracted	High confidence	250.538	234.401	16.137
	translin-associated protein x (translin-associated factor x). [swissprot;acc:q99598]	0	Divided		20875	20495	1.01854
	zinc finger protein 264. [swissprot;acc:o43296]		Subtracted	Low confidence	4253.34	4850.04	596.7
460	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]			High confidence	18667	18500	167
	mitochondrial 28s ribosomal protein s6 (mrp-s6). [swissprot;acc:p82932]		Divided		20914	20558	1.01732
	proactivator polypeptide precursor [contains: saposin a (protein a); saposin b (sphingolipid activator protein 1) (sap-1) (cerebroside sulfate activator) (csact) (dispersin) (sulfatide/gm1 activator); saposin c (co-beta-glucosidase) (a1 activator) (glucosylceramidase activator) (sphingolipid activator protein 2) (sap-2); saposin d (protein c) (component c)]. [swissprot;acc:p07602]	1		Low confidence	209.188	202.243	1.03434
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]		Subtracted	High confidence	186.52	170.42	16.1
	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]			Low confidence	208.29	201.499	6.791
	splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428]		Divided	High confidence	223.648	207.62	1.0772
	synaptotagmin xiv. [refseq;acc:nm_153262]	0		Low confidence	9414	10068.8	1.06956
	zinc finger protein 10 (zinc finger protein kox1) (fragment). [swissprot;acc:p21506]		Subtracted		4253.18	4849.87	596.69
461	huntingtin interacting protein c. [refseq;acc:nm_012272]	1	Divided		201.429	194.776	1.03416

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.