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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

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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 3558 to 3607 of 12912 in total

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

Rank	description	Value Type	red	green	network_comparison
890	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	Squared	18178.2	21081.9	1.15974
	syntaxin 7. [swissprot;acc:o15400]	Ranked	217.181	209.012	1.03908
	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775]	Measured	5350.87	5896.82	1.10203
891	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]		5385.04	5933.65	1.10188
	polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025]	Rooted	56.7818	60.2369	1.06085
	rw1 protein (fragment). [swissprot;acc:q92545]	Squared	18178.2	21081.9	1.15974
	small gtp-binding tumor suppressor 1. [refseq;acc:nm_145173]	Ranked	212.028	204.055	1.03907
892	cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701]	Rooted	56.7817	60.2369	1.06085
	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	Measured	6784.67	7475.48	1.10182
	di-ras2. [refseq;acc:nm_017594]	Ranked	212.028	204.055	1.03907
	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8]	Squared	26312	30514.1	1.1597
893	e-1 enzyme. [refseq;acc:nm_021204]	Measured	6603.09	7274.72	1.10171
	glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711]	Rooted	56.781	60.2344	1.06082
	myc proto-oncogene protein (c-myc). [swissprot;acc:p01106]	Ranked	227.585	219.037	1.03903
	sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676]	Squared	26312	30514.1	1.1597
894	parafibromin. [refseq;acc:nm_024529]	Measured	4331.17	4771.22	1.1016
	phenylalanyl-trna synthetase alpha chain (ec 6.1.1.20) (phenylalanine- -trna ligase alpha chain) (phers) (cml33). [swissprot;acc:q9y285]	Ranked	217.491	209.323	1.03902
	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [swissprot;acc:q92997]	Squared	20322.5	23567.1	1.15966
	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403]	Rooted	56.2142	59.6282	1.06073
895	exocyst complex component sec8. [swissprot;acc:q96a65]		63.2983	67.1422
	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	Measured	10247.8	11289	1.1016
	leucyl-trna synthetase. [refseq;acc:nm_020117]	Squared	21830.4	25308.2	1.15931
	phenylalanine-trna synthetase. [refseq;acc:nm_006567]	Ranked	217.491	209.323	1.03902
896	dna-directed rna polymerase ii 13.3 kda polypeptide (ec 2.7.7.6) (rpb11). [swissprot;acc:p52435]		230.811	239.785	1.03888
	probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031]	Squared	21830.4	25308.3	1.15931
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	Measured	5208.27	5737.17	1.10155
	thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]	Rooted	56.2142	59.6282	1.06073
897	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	Ranked	272.878	283.472	1.03882
	glucose-6-phosphate isomerase (ec 5.3.1.9) (gpi) (phosphoglucose isomerase) (pgi) (phosphohexose isomerase) (phi) (neuroleukin) (nlk) (sperm antigen-36) (sa-36). [swissprot;acc:p06744]	Squared	29924.3	34690.9	1.15929
	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	Measured	5929.48	6531.48	1.10153
	nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [swissprot;acc:p55769]	Rooted	56.2142	59.6282	1.06073
898	60s acidic ribosomal protein p1. [swissprot;acc:p05386]	Ranked	229.171	238.048	1.03874
	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]	Measured	5929.55	6531.52	1.10152
	nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [refseq;acc:nm_012345]	Rooted	56.2142	59.6282	1.06073
	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	Squared	21156.1	24524.1	1.1592
899	6-phosphogluconolactonase (ec 3.1.1.31) (6pgl). [swissprot;acc:o95336]		29345.7	34004.2	1.15875
	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	Rooted	66.5785	70.6139	1.06061
	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]	Measured	5929.55	6531.52	1.10152
	thioredoxin domain-containing 2; sperm-specific thioredoxin; thioredoxin domain-containing 2 (spermatozoa). [refseq;acc:nm_032243]	Ranked	229.171	238.048	1.03874
900	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	Measured	4713.58	4279.17	1.10152
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	Rooted	66.5785	70.6139	1.06061
	thioredoxin (atl-derived factor) (adf) (surface associated sulphydryl protein) (sasp). [swissprot;acc:p10599]	Ranked	229.171	238.048	1.03874
	topoisomerase (dna) ii binding protein. [refseq;acc:nm_007027]	Squared	28068.5	32522.9	1.1587
901	acyl-coenzyme a oxidase 1, peroxisomal (ec 1.3.3.6) (palmitoyl-coa oxidase) (aox). [swissprot;acc:q15067]
	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	Rooted	66.5785	70.6139	1.06061
	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	Measured	5929.61	6531.55	1.10151
	structure-specific recognition protein 1 (ssrp1) (recombination signal sequence recognition protein) (t160) (chromatin-specific transcription elongation factor 80 kda subunit) (fact 80 kda subunit). [swissprot;acc:q08945]	Ranked	237.62	228.762	1.03872
902	atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]	Squared	28068.5	32522.9	1.1587
	chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]	Ranked	237.62	228.762	1.03872
	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Measured	10246.1	11285.8	1.10147

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.