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	Value Type	Network Comparison Type	red	Interaction Map	green	Filtered	network_comparison

Results: HTML CSV LaTeX

Showing element 467 to 516 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
234	40s ribosomal protein s23. [swissprot;acc:p39028]	Subtracted	243.944	268.195	24.251
	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Divided	287.41	256.835	1.11905
235	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	Subtracted	243.944	268.195	24.251
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Divided	227.357	254.15	1.11785
236	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
	pp3111 protein. [refseq;acc:nm_022156]	Divided	227.357	254.15	1.11785
237	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	Subtracted	242.011	266.18	24.169
	syntaxin 18. [swissprot;acc:q9p2w9]	Divided	227.357	254.15	1.11785
238	metastasis-associated protein mta1. [swissprot;acc:q13330]	Subtracted	252.512	228.356	24.156
	rd protein. [swissprot;acc:p18615]	Divided	227.357	254.15	1.11785
239	dna-directed rna polymerase ii largest subunit (ec 2.7.7.6) (rpb1). [swissprot;acc:p24928]	Subtracted	243.817	267.962	24.145
	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Divided	227.357	254.15	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	252.39	228.297	24.093
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	Divided	227.357	254.15	1.11785
	epithelial-cadherin precursor (e-cadherin) (uvomorulin) (cadherin-1) (cam 120/80). [swissprot;acc:p12830]	Subtracted	241.892	265.96	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	227.357	254.15	1.11785
243	60s ribosomal protein l23a. [swissprot;acc:p29316]	Subtracted	241.884	265.945	24.061
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Divided	227.357	254.15	1.11785
244	60s ribosomal protein l5. [swissprot;acc:p46777]	Subtracted	241.899	265.924	24.025
	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	Divided	227.357	254.15	1.11785
245	60s ribosomal protein l19. [swissprot;acc:p14118]	Subtracted	240.73	264.729	23.999
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Divided	226.109	202.333	1.11751
246	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Subtracted	243.583	267.528	23.945
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Divided	237.312	212.363	1.11748
247	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	ns1-associated protein 1. [refseq;acc:nm_006372]	Divided	237.302	212.41	1.11719
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Subtracted	226.109	202.333	23.776
250	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Divided	237.302	212.41	1.11719
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Subtracted	210.693	186.95	23.743
251	40s ribosomal protein s20. [swissprot;acc:p17075]		243.5	267.21	23.71
	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	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]		237.292	212.457	1.11689
	mad protein (max dimerizer). [swissprot;acc:q05195]	Subtracted	228	204.333	23.667
253		Divided			1.11583
	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	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]		227.999	204.357
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Divided	200.691	179.88	1.11569
255	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Subtracted	227.999	204.366	23.633
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Divided	200.691	179.88	1.11569
256	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	Subtracted	227.999	204.37	23.629
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	Divided		204.357	1.11569
257	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]		200.691	179.88
	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	Subtracted	242.14	265.697	23.557
258	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Divided	227.999	204.366	1.11564

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.