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

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Showing element 2075 to 2124 of 3228 in total

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

Rank	network_comparison	red	description	green
2075	1.05579	3614.91	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	3423.89
2076		5746.65	af-6 protein. [swissprot;acc:p55196]	6067.27
2077		3614.91	60s ribosomal protein l34. [swissprot;acc:p49207]	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	1.05577	5837.34	r3h domain protein 1. [swissprot;acc:q15032]	6162.91
2081	1.05568	6318.3	paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [swissprot;acc:p26367]	6670.1
2082	1.05559	5800.93	ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792]	6123.38
2083	1.05558	5799.84	ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	6122.18
2084		5800.22		6122.6
2085	1.05552	5835.4	channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	6159.4
2086		5835.44	presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352]	6159.45
2087		5835.45	presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796]	6159.46
2088		5835.15	presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959]	6159.11
2089	1.05535	5775.22	putative gtp-binding protein ptd004 (pro2455). [swissprot;acc:q9ntk5]	6094.89
2090	1.05527	5817.07	kh-type splicing regulatory protein (fuse binding protein 2); kh-type splicing regulatory protein (fuse-binding protein 2). [refseq;acc:nm_003685]	6138.59
2091	1.05526	5247.76	maguk p55 subfamily member 6 (veli-associated maguk 1) (vam-1). [swissprot;acc:q9nzw5]	5537.75
2092	1.05525	5817.41	far upstream element-binding protein; far upstream element binding protein; fuse-binding protein. [refseq;acc:nm_003902]	6138.8
2093	1.05524	5817.56	fuse binding protein 3 (fragment). [sptrembl;acc:q92946]	6138.9
2094	1.05522	6682.05	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]	7051.02
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	1.05512	6024.47	polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481]	6356.56
2098			similar to expressed sequence ai415388 (fragment). [sptrembl;acc:q8n428]
2099	1.05495	3544.03	methionine aminopeptidase 1 (ec 3.4.11.18) (metap 1) (map 1) (peptidase m 1). [swissprot;acc:p53582]	3359.43
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	1.05493	5241.34	maguk p55 subfamily member 2 (mpp2 protein) (discs, large homolog 2). [swissprot;acc:q14168]	5529.25
2102		4860.34	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]	5127.3
2103	1.05486	6847.82	asparaginyl-trna synthetase, cytoplasmic (ec 6.1.1.22) (asparagine-- trna ligase) (asnrs). [swissprot;acc:o43776]	7223.51
2104	1.05481	6916.14	protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237]	7295.24
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	1.0547	5776.79	rna-binding protein 9 (rna binding motif protein 9) (hexaribonucleotide binding protein 2) (repressor of tamoxifen transcriptional activity). [swissprot;acc:o43251]	6092.77
2114	1.05466	3617.81	60s ribosomal protein l3-like. [swissprot;acc:q92901]	3430.31
2115	1.0546	3672.49	60s ribosomal protein l23 (l17). [swissprot;acc:p23131]	3482.34
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		5778.16	ataxin 2-binding protein. [swissprot;acc:q9nwb1]	6093.65
2118	1.05447	5620.55	guanylate kinase (ec 2.7.4.8) (gmp kinase). [swissprot;acc:q16774]	5926.71
2119	1.05434	5976.96	lamin a/c (70 kda lamin). [swissprot;acc:p02545]	6301.73
2120		6951.29	c316g12.2 (novel protein similar to predicted yeast, worm and archae- bacterial proteins) (similar to und313) (s. cervisiae) (hypothetical protein). [sptrembl;acc:q9ujk0]	7329
2121	1.05433	5977.03	centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]	6301.76
2122			centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]
2123			centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]
2124	1.05432	5977.09	lamin b1. [swissprot;acc:p20700]	6301.79

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.