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	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 1844 to 1893 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
922	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	Subtracted	215.665	207.942	7.723
923	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]		193.114	185.412	7.702
	map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]	Divided	236.741	245.547	1.0372
924	meiotic recombination protein spo11. [swissprot;acc:q9y5k1]
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	Subtracted	238.725	231.059	7.666
925	pef protein with a long n-terminal hydrophobic domain (peflin). [refseq;acc:nm_012392]	Divided	215.665	207.942	1.03714
	protein bap28. [swissprot;acc:q9h583]	Subtracted	244.312	236.647	7.665
926	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Divided	217.942	210.139	1.03713
	ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	Subtracted	212.952	205.292	7.66
927	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Divided	217.942	210.139	1.03713
	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	Subtracted	220.246	212.618	7.628
928	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	Divided	225.976	218.017	1.03651
	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	Subtracted	220.246	212.618	7.628
929	apoptosis antagonizing transcription factor. [refseq;acc:nm_012138]		243.045	235.422	7.623
	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	Divided	225.955	218.015	1.03642
930	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	Subtracted	233.402	225.782	7.62
	pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	Divided	231.357	239.778	1.0364
931	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]		159.13	164.917	1.03637
	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	Subtracted	228.953	221.421	7.532
932	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	Divided	225.939	218.013	1.03636
	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]	Subtracted	228.953	221.421	7.532
933	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	Divided	159.165	164.951	1.03635
	probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	Subtracted	242.978	235.518	7.46
934	nucleolar rna-associated protein alpha isoform. [refseq;acc:nm_022917]	Divided	242.024	233.544	1.03631
	target of myb protein 1. [swissprot;acc:o60784]	Subtracted	217.254	209.824	7.43
935	huntingtin-associated protein-interacting protein (duo protein). [swissprot;acc:o60229]		217.253	209.826	7.427
	sirtuin 7; sir2-related protein type 7; sirtuin type 7; sirtuin (silent mating type information regulation 2, s.cerevisiae, homolog) 7; silent mating type information regulation 2, s.cerevisiae, homolog 7; sirtuin silent mating type information regulation 2 homolog 7 (s. cerevisiae). [refseq;acc:nm_016538]	Divided	232.473	224.372	1.03611
936	casein kinase ii beta chain (ck ii) (phosvitin) (g5a). [swissprot;acc:p13862]
	triple functional domain protein (ptprf interacting protein). [swissprot;acc:o75962]	Subtracted	217.253	209.827	7.426
937	splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874]	Divided	220.246	212.618	1.03588
	target of myb1-like 2; target of myb1 (chicken) homolog-like 2. [refseq;acc:nm_144678]	Subtracted	217.252	209.83	7.422
938	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]		212.442	205.087	7.355
	splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459]	Divided	220.246	212.618	1.03588
939	breast cancer type 1 susceptibility protein. [swissprot;acc:p38398]		216.501	224.27
	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]	Subtracted	212.44	205.085	7.355
940	calcium-dependent protease, small subunit (calpain regulatory subunit) (calcium-activated neutral proteinase) (canp). [swissprot;acc:p04632]	Divided	212.442	205.088	1.03586
		Subtracted			7.354
941	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Divided	212.437	205.083	1.03586
		Subtracted			7.354
942	grancalcin. [swissprot;acc:p28676]	Divided	212.442	205.088	1.03586
		Subtracted			7.354
943	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]		212.437	205.083
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Divided	212.442	205.087	1.03586
944	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	Subtracted	212.51	205.191	7.319
	programmed cell death protein 6 (probable calcium-binding protein alg- 2). [swissprot;acc:o75340]	Divided	212.437	205.083	1.03586
945	brg1-binding protein eld/osa1; eld (eyelid)/osa protein. [refseq;acc:nm_020732]		212.44	205.085
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]	Subtracted	229.116	221.823	7.293
946	dynein intermediate chain 2, cytosolic (dh ic-2) (cytoplasmic dynein intermediate chain 2). [swissprot;acc:q13409]		225.557	218.271	7.286
	histone h4. [swissprot;acc:p02304]	Divided	227.765	219.902	1.03576
947	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]		212.51	205.191	1.03567

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.