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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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Rank	Gene	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	network_comparison

Results: HTML CSV LaTeX

Showing element 6458 to 6507 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
404	nucleotide binding protein 2 (nbp 2). [swissprot;acc:q9y5y2]	Rooted	Divided	1	59.6834	65.6741	1.10037
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Ranked	Subtracted	0	10598.5	10945.3	346.8
	spir-2 protein (fragment). [sptrembl;acc:q8wwl2]	Measured			31.1429	56.278	25.1351
	sprouty homolog 4 (spry-4). [swissprot;acc:q9c004]	Rooted			25.6478	26.3666	0.7188
	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Measured	Divided		1229.57	1278.36	1.03968
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Squared			84448.4	89963.1	1.0653
	udp-glucuronosyltransferase 2b11 precursor, microsomal (ec 2.4.1.17) (udpgt). [swissprot;acc:o75310]	Ranked			9783.63	10111.2	1.03348
405	adenylosuccinate synthase-like 1. [refseq;acc:nm_152328]	Squared		1	26822.2	32858.1	1.22503
	alpha-1-acid glycoprotein 2 precursor (agp 2) (orosomucoid 2) (omd 2). [swissprot;acc:p19652]	Rooted	Subtracted	0	32.2451	32.9629	0.7178
	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]		Divided	1	116.576	105.948	1.10031
	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]		Subtracted		48.0045	54.0843	6.0798
	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Ranked	Divided		207.931	226.209	1.0879
	gaba(a) receptor-associated protein; gaba(a)-receptor-associated protein. [refseq;acc:nm_007278]		Subtracted		65.4586	83.0461	17.5875
	guanine nucleotide-binding protein g(y), alpha subunit (alpha-11). [swissprot;acc:p29992]	Measured			1836.71	907.546	929.164
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Squared	Divided	0	84951.4	90481	1.06509
	integral membrane protein cii-3b. [sptrembl;acc:o75609]	Measured			2218.63	2304.22	1.03858
	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]			1	5201.41	4479.76	1.16109
	phosphoglycerate kinase 1 (ec 2.7.2.3) (primer recognition protein 2) (prp 2). [swissprot;acc:p00558]	Squared	Subtracted		28192	33985.3	5793.3
	seven in absentia homolog 1. [refseq;acc:nm_003031]	Ranked		0	9854.67	10201.4	346.73
	similar to cg7020 gene product (fragment). [sptrembl;acc:q96ib4]	Measured			2806.38	2782.56	23.82
	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	Rooted	Divided		17.5059	16.9709	1.03152
	transcription factor btf3 homolog 3. [swissprot;acc:q13892]	Squared	Subtracted		31.0895	37.1241	6.0346
	udp-glucuronosyltransferase 2b4 precursor, microsomal (ec 2.4.1.17) (udpgt) (hyodeoxycholic acid) (hlug25) (udpgth-1). [swissprot;acc:p06133]	Ranked	Divided		9783.63	10111.2	1.03348
406	60s ribosomal protein l12. [swissprot;acc:p30050]		Subtracted		10196.9	9857.79	339.11
		Rooted	Divided	1	49.9858	45.4433	1.09996
	dead/h (asp-glu-ala-asp/his) box polypeptide 11; dead/h box-11 (chl1-related helicase gene-1); yeast chl1 homolog. [refseq;acc:nm_030655]		Subtracted	0	21.8861	22.6039	0.7178
	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	Measured			1915.69	1892.44	23.25
	fibrillin 3. [refseq;acc:nm_032447]	Squared	Divided		48035.2	45133.4	1.06429
	glutamyl aminopeptidase (ec 3.4.11.7) (eap) (aminopeptidase a) (apa) (differentiation antigen gp160). [swissprot;acc:q07075]	Ranked			9783.63	10111.2	1.03348
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Measured	Subtracted	1	1836.71	907.564	929.146
	homeobox protein hox-d9 (hox-4c) (hox-5.2). [swissprot;acc:p28356]	Squared			32208.8	37986.6	5777.8
	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]	Ranked			237.109	254.667	17.558
	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	Rooted			56.2615	62.2958	6.0343
	serine protease htra2, mitochondrial precursor (ec 3.4.21.-) (high temperature requirement protein a2) (htra2) (omi stress-regulated endoprotease) (serine proteinase omi). [swissprot;acc:o43464]	Squared	Divided		18995.7	23245.6	1.22373
	syntaxin 1a (neuron-specific antigen hpc-1). [swissprot;acc:q16623]		Subtracted	0	6.45653	12.2937	5.83717
	thymic stromal co-transporter. [refseq;acc:nm_033051]	Measured	Divided	1	5201.41	4479.76	1.16109
	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186]	Ranked			265.634	244.304	1.08731
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	Rooted		0	44.9117	43.5558	1.03113
	u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695]	Measured			2363.32	2454.04	1.03839
407	28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933]	Ranked		1	239.75	260.544	1.08673
	60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]	Rooted			49.9856	45.4431	1.09996
	actin, cytoplasmic 2 (gamma-actin). [swissprot;acc:p02571]		Subtracted	0	21.6987	22.4088	0.7101
	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	Ranked			10195.5	9856.7	338.8
	glycogenin-2 (ec 2.4.1.186) (gn-2) (gn2). [swissprot;acc:o15488]	Squared	Divided		192242	204096	1.06166
	guanine nucleotide-binding protein g(z), alpha subunit (g(x) alpha chain) (gz-alpha). [swissprot;acc:p19086]	Measured	Subtracted	1	1836.76	907.741	929.019
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]		Divided	0	3614.24	3481.87	1.03802
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Rooted			6.9282	7.14143	1.03078
	nadh-ubiquinone oxidoreductase b14 subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b14) (ci-b14). [swissprot;acc:p56556]	Squared	Subtracted	1	32193.3	37967.7	5774.4
	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	Ranked			237.109	254.667	17.558
	oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348]	Rooted			80.2562	86.277	6.0208

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.