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	green	red	network_comparison

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

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.