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 2075 to 2124 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	red	green	network_comparison
2075	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	3614.91	3423.89	1.05579
2076	af-6 protein. [swissprot;acc:p55196]	5746.65	6067.27
2077	60s ribosomal protein l34. [swissprot;acc:p49207]	3614.91	3423.89
2078	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]
2079	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]
2080	r3h domain protein 1. [swissprot;acc:q15032]	5837.34	6162.91	1.05577
2081	paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367]	6318.3	6670.1	1.05568
2082	ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792]	5800.93	6123.38	1.05559
2083	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	5799.84	6122.18	1.05558
2084		5800.22	6122.6
2085	channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	5835.4	6159.4	1.05552
2086	presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352]	5835.44	6159.45
2087	presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796]	5835.45	6159.46
2088	presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959]	5835.15	6159.11
2089	putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5]	5775.22	6094.89	1.05535
2090	kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685]	5817.07	6138.59	1.05527
2091	maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5]	5247.76	5537.75	1.05526
2092	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	5817.41	6138.8	1.05525
2093	fuse binding protein 3 (fragment). [sptrembl;acc:q92946]	5817.56	6138.9	1.05524
2094	nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991]	6682.05	7051.02	1.05522
2095	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]
2096	germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]
2097	polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481]	6024.47	6356.56	1.05512
2098	similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428]
2099	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	3544.03	3359.43	1.05495
2100	methionine aminopeptidase 2 (ec 3.4.11.18) (metap 2) (peptidase m 2) (initiation factor 2 associated 67 kda glycoprotein) (p67) (p67eif2). [swissprot;acc:p50579]
2101	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	5241.34	5529.25	1.05493
2102	c-1-tetrahydrofolate synthase, cytoplasmic (c1-thf synthase) [includes: methylenetetrahydrofolate dehydrogenase (ec 1.5.1.5); methenyltetrahydrofolate cyclohydrolase (ec 3.5.4.9); formyltetrahydrofolate synthetase (ec 6.3.4.3)]. [swissprot;acc:p11586]	4860.34	5127.3
2103	asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776]	6847.82	7223.51	1.05486
2104	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	6916.14	7295.24	1.05481
2105	3-hydroxyanthranilate 3,4-dioxygenase (ec 1.13.11.6) (3-hao) (3-hydroxyanthranilic acid dioxygenase) (3-hydroxyanthranilate oxygenase). [swissprot;acc:p46952]
2106	zinc finger protein-like 1; zinc-finger protein in men1 region. [refseq;acc:nm_006782]
2107	hus1 checkpoint protein; hus1 (s. pombe) checkpoint homolog; hus1+-like protein. [refseq;acc:nm_004507]
2108	hyaluronan binding protein 4; intracellular antigen detected by monoclonal antibody ki-1; intracellular hyaluronan-binding protein; chromodomain helicase dna binding protein 3 interacting protein. [refseq;acc:nm_014282]
2109	prolyl 4-hydroxylase alpha-1 subunit precursor (ec 1.14.11.2) (4-ph alpha-1) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-1 subunit). [swissprot;acc:p13674]
2110	homeobox prospero-like protein prox1 (prox 1). [swissprot;acc:q92786]
2111	rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853]
2112	prolyl 4-hydroxylase alpha-2 subunit precursor (ec 1.14.11.2) (4-ph alpha-2) (procollagen-proline,2-oxoglutarate-4-dioxygenase alpha-2 subunit). [swissprot;acc:o15460]
2113	rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251]	5776.79	6092.77	1.0547
2114	60s ribosomal protein l3-like. [swissprot;acc:q92901]	3617.81	3430.31	1.05466
2115	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	3672.49	3482.34	1.0546
2116	brca2 and cdkn1a-interacting protein isoform bccipalpha; brca2 and cdkn1a-interacting protein; cdk inhibitor p21 binding protein; bccipalpha; bccipbeta; tok-1alpha; tok-1beta. [refseq;acc:nm_016567]
2117	ataxin 2-binding protein. [swissprot;acc:q9nwb1]	5778.16	6093.65
2118	guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774]	5620.55	5926.71	1.05447
2119	lamin a/c (70 kda lamin). [swissprot;acc:p02545]	5976.96	6301.73	1.05434
2120	c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0]	6951.29	7329
2121	centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]	5977.03	6301.76	1.05433
2122	centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
2123	centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]
2124	lamin b1. [swissprot;acc:p20700]	5977.09	6301.79	1.05432

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.