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

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

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.