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

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Showing element 462 to 511 of 6456 in total

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

Rank	Hugo	description	Network Comparison Type	red	green	network_comparison
231	SHCBP1	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Divided	239.336	267.881	1.11927
232	BCAR3	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Subtracted	226.401	202.094	24.307
	CSRP2	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	Divided	239.336	267.879	1.11926
233	no value	60s ribosomal protein l7. [swissprot;acc:p18124]	Subtracted	235.727	259.984	24.257
	CSRP3	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	Divided	239.32	267.842	1.11918
234	CHRAC1	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]		287.41	256.835	1.11905
	RPS23	40s ribosomal protein s23. [swissprot;acc:p39028]	Subtracted	243.944	268.195	24.251
235	MRPS12	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]
	PAH	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Divided	227.357	254.15	1.11785
236	DUS1L	pp3111 protein. [refseq;acc:nm_022156]
	RBBP7	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	Subtracted	252.644	228.42	24.224
237	MRPL3	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]		242.011	266.18	24.169
	STX18	syntaxin 18. [swissprot;acc:q9p2w9]	Divided	227.357	254.15	1.11785
238	no value	rd protein. [swissprot;acc:p18615]
	MTA1	metastasis-associated protein mta1. [swissprot;acc:q13330]	Subtracted	252.512	228.356	24.156
239	GSTO1	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Divided	227.357	254.15	1.11785
	POLR2A	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Subtracted	243.817	267.962	24.145
240	AIG1	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	Divided	227.357	254.15	1.11785
	RBBP4	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	228.297	24.093
241	ATP5F1	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	Divided	227.357	254.15	1.11785
	CDH1	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Subtracted	241.892	265.96	24.068
242	no value	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]			265.959	24.067
	DNAJC12	j domain containing protein 1. [swissprot;acc:q9ukb3]	Divided	227.357	254.15	1.11785
243	no value	60s ribosomal protein l23a. [swissprot;acc:p29316]	Subtracted	241.884	265.945	24.061
	SNX13	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Divided	227.357	254.15	1.11785
244	GSTO2	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
	RPL5	60s ribosomal protein l5. [swissprot;acc:p46777]	Subtracted	241.899	265.924	24.025
245	RPL19	60s ribosomal protein l19. [swissprot;acc:p14118]		240.73	264.729	23.999
	SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Divided	226.109	202.333	1.11751
246	no value	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Subtracted	243.583	267.528	23.945
	EIF4G3	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Divided	237.312	212.363	1.11748
247	no value	60s ribosomal protein l12. [swissprot;acc:p30050]	Subtracted	243.583	267.527	23.944
		rna-binding protein. [refseq;acc:nm_019027]	Divided	237.302	212.41	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	243.583	267.527	23.944
249	SNRPD3	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]		226.109	202.333	23.776
	SYNCRIP	ns1-associated protein 1. [refseq;acc:nm_006372]	Divided	237.302	212.41	1.11719
250	HNRNPR	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
	PLDN	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Subtracted	210.693	186.95	23.743
251	RPS20	40s ribosomal protein s20. [swissprot;acc:p17075]		243.5	267.21	23.71
	SLC15A1	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Divided	186.172	166.661	1.11707
252	EIF4G1	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]		237.292	212.457	1.11689
	MXD1	mad protein (max dimerizer). [swissprot;acc:q05195]	Subtracted	228	204.333	23.667
253			Divided			1.11583
	NFYB	nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [swissprot;acc:p25208]	Subtracted	251.679	228.037	23.642
254	MXI1	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]		227.999	204.357
	STT3B	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Divided	200.691	179.88	1.11569
255	MXD4	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Subtracted	227.999	204.366	23.633
	STT3A	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Divided	200.691	179.88	1.11569
256	MXI1	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]		227.999	204.357

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
- Hugo is the HGNC identifier if it exists
- 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.