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	red	green	network_comparison

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Showing element 6308 to 6357 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
395	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Ranked	Divided	1	218.827	238.407	1.08948
	dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9]	Measured	Subtracted	0	3889.5	3919.25	29.75
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Ranked	Divided		10195.5	9856.7	1.03437
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-3 subunit. [swissprot;acc:p29798]	Measured	Subtracted	1	1834.36	895.194	939.166
	histone h2b.s (h2b/s). [swissprot;acc:p57053]		Divided	0	2131.83	2218.82	1.04081
	leucine-rich repeat-containing protein 15 precursor (hlib). [swissprot;acc:q8tf66]	Squared	Subtracted	1	26157.6	20236.2	5921.4
	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]		Divided		17254.4	21218.1	1.22972
	phosducin-like protein (phlp). [swissprot;acc:q13371]	Ranked	Subtracted		207.908	226.218	18.31
	probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	Rooted		0	93.5322	92.7071	0.8251
	protein translation factor sui1 homolog (sui1iso1). [swissprot;acc:p41567]		Divided	1	50.0423	45.4523	1.10098
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Squared		0	6777.96	6288.98	1.07775
	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [swissprot;acc:q13435]	Rooted	Subtracted	1	58.0752	64.23	6.1548
	splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164]	Measured	Divided		4532.73	5269.33	1.16251
396	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Ranked		0	10194.8	9856.12	1.03436
	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Rooted		1	116.797	106.111	1.10071
	dok-like protein. [refseq;acc:nm_024872]		Subtracted		63.2134	69.352	6.1386
	fem-1 homolog b; fem-1-like death receptor binding protein; fem-1 (c.elegans) homolog b. [refseq;acc:nm_015322]	Squared			26157.6	20236.2	5921.4
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-8 subunit (gamma-9). [swissprot;acc:q9uk08]	Measured			1834.52	895.507	939.013
	histone h2b. [refseq;acc:nm_175055]		Divided	0	2131.91	2218.89	1.0408
	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	Rooted	Subtracted		197.901	198.708	0.807
	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	Squared	Divided	1	17256.5	21219.6	1.22966
	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]		Subtracted	0	21.8736	31.1879	9.3143
	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Ranked	Divided	1	240.801	262.34	1.08945
	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	Squared		0	6749.52	6272.46	1.07606
	replication protein a 70 kda dna-binding subunit (rp-a) (rf-a) (replication factor-a protein 1) (single-stranded dna-binding protein). [swissprot;acc:p27694]	Ranked	Subtracted	1	207.908	226.218	18.31
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Measured	Divided		6563.65	7627.29	1.16205
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]	Rooted		0	32.0372	30.9782	1.03419
	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Ranked	Subtracted		7769.96	8139.71	369.75
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Measured			112.666	141.702	29.036
397	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	Ranked	Divided		10006.9	9676.53	1.03414
	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	Rooted	Subtracted	1	63.2134	69.352	6.1386
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Squared	Divided	0	80280.6	74715.1	1.07449
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-5 subunit. [swissprot;acc:p30670]	Measured	Subtracted	1	1834.59	895.633	938.957
	histone h2b.e (h2b/e). [swissprot;acc:q99879]		Divided	0	2131.93	2218.9	1.04079
	leucine-rich repeat protein lrrc3 precursor. [swissprot;acc:q9by71]	Squared	Subtracted	1	26157.6	20236.2	5921.4
	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]		Divided		17257.5	21220.3	1.22963
	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	Measured			5367.04	6233.12	1.16137
	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	Squared	Subtracted	0	10.3503	19.2071	8.8568
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Rooted	Divided	1	116.792	106.107	1.1007
	replication protein a 32 kda subunit (rp-a) (rf-a) (replication factor-a protein 2). [swissprot;acc:p15927]	Ranked	Subtracted		207.908	226.218	18.31
	ribosomal protein s27-like protein; 40s ribosomal protein s27 isoform. [refseq;acc:nm_015920]			0	9565.54	9935.19	369.65
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	Rooted			41.788	42.5828	0.7948
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]		Divided		18.8643	18.2434	1.03403
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	Ranked		1	110.689	101.613	1.08932
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	Measured	Subtracted	0	112.666	141.702	29.036
398	basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811]	Rooted			15.297	14.5086	0.7884
	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]			1	63.2134	69.352	6.1386
	glycerol kinase (ec 2.7.1.30) (atp:glycerol 3-phosphotransferase) (glycerokinase) (gk). [swissprot;acc:p32189]	Ranked	Divided	0	16699.2	17267.9	1.03406
	guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-10 subunit. [swissprot;acc:p50151]	Measured	Subtracted	1	1834.63	895.697	938.933
	histone h2b.c (h2b/c). [swissprot;acc:q99880]		Divided	0	2132.04	2218.98	1.04078

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.