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	Network Comparison Type	Value Type	Interaction Map	Filtered	network_comparison	green	red

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Showing element 451 to 500 of 6456 in total

Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	network_comparison	green	red
226	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]	Divided	1.12187	269.238	239.991
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	Subtracted	24.52	266.673	242.153
227	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]		24.478	268.604	244.126
	thrombospondin 3 precursor. [swissprot;acc:p49746]	Divided	1.12186	269.234	239.99
228	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]	Subtracted	24.478	268.604	244.126
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Divided	1.12036	202.088	226.411
229	60s ribosomal protein l3-like. [swissprot;acc:q92901]	Subtracted	24.468	266.663	242.195
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Divided	1.12028	202.094	226.401
230	cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291]		1.11934	267.915	239.35
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]	Subtracted	24.323	267.017	242.694
231	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Divided	1.11927	267.881	239.336
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	Subtracted	24.323	202.088	226.411
232	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]		24.307	202.094	226.401
	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Divided	1.11926	267.879	239.336
233	60s ribosomal protein l7. [swissprot;acc:p18124]	Subtracted	24.257	259.984	235.727
	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Divided	1.11918	267.842	239.32
234	40s ribosomal protein s23. [swissprot;acc:p39028]	Subtracted	24.251	268.195	243.944
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Divided	1.11905	256.835	287.41
235	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	Subtracted	24.251	268.195	243.944
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Divided	1.11785	254.15	227.357
236	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Subtracted	24.224	228.42	252.644
	pp3111 protein. [refseq;acc:nm_022156]	Divided	1.11785	254.15	227.357
237	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Subtracted	24.169	266.18	242.011
	syntaxin 18. [swissprot;acc:q9p2w9]	Divided	1.11785	254.15	227.357
238	metastasis-associated protein mta1. [swissprot;acc:q13330]	Subtracted	24.156	228.356	252.512
	rd protein. [swissprot;acc:p18615]	Divided	1.11785	254.15	227.357
239	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Subtracted	24.145	267.962	243.817
	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Divided	1.11785	254.15	227.357
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
	chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	Subtracted	24.093	228.297	252.39
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	Divided	1.11785	254.15	227.357
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Subtracted	24.068	265.96	241.892
242	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]		24.067	265.959
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Divided	1.11785	254.15	227.357
243	60s ribosomal protein l23a. [swissprot;acc:p29316]	Subtracted	24.061	265.945	241.884
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Divided	1.11785	254.15	227.357
244	60s ribosomal protein l5. [swissprot;acc:p46777]	Subtracted	24.025	265.924	241.899
	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	Divided	1.11785	254.15	227.357
245	60s ribosomal protein l19. [swissprot;acc:p14118]	Subtracted	23.999	264.729	240.73
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Divided	1.11751	202.333	226.109
246	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Subtracted	23.945	267.528	243.583
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Divided	1.11748	212.363	237.312
247	60s ribosomal protein l12. [swissprot;acc:p30050]	Subtracted	23.944	267.527	243.583
	rna-binding protein. [refseq;acc:nm_019027]	Divided	1.11719	212.41	237.302
248	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Subtracted	23.944	267.527	243.583
249	ns1-associated protein 1. [refseq;acc:nm_006372]	Divided	1.11719	212.41	237.302
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Subtracted	23.776	202.333	226.109
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Divided	1.11719	212.41	237.302
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Subtracted	23.743	186.95	210.693

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.