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

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Showing element 2080 to 2129 of 12912 in total

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

Rank	Value Type	description	red	green	network_comparison
520	Rooted	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	61.1902	66.6503	1.08923
521	Measured	u4/u6-associated rna splicing factor. [refseq;acc:nm_004698]	5390.78	6142.07	1.13937
	Ranked	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [swissprot;acc:q9npd3]	215.237	230.07	1.06891
	Squared	carboxypeptidase a5. [refseq;acc:nm_080385]	53174	44377.4	1.19822
	Rooted	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]	61.1902	66.6503	1.08923
522	Measured	glycogen [starch] synthase, liver (ec 2.4.1.11). [swissprot;acc:p54840]	9634.98	10976.2	1.1392
	Ranked	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [refseq;acc:nm_002669]	222.893	208.523	1.06891
	Squared	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [swissprot;acc:p15086]	53174	44377.4	1.19822
	Rooted	septin 10 isoform 1. [refseq;acc:nm_144710]	113.733	123.871	1.08914
523	Measured	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	10640.2	12117.8	1.13887
	Ranked	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [swissprot;acc:q13868]	215.237	230.07	1.06891
	Squared	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [swissprot;acc:q07837]	53174	44377.4	1.19822
	Rooted	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	66.377	72.2842	1.08899
524	Measured	aquaporin 5. [swissprot;acc:p55064]	10640	12117.6	1.13887
	Ranked	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]	215.237	230.07	1.06891
	Squared	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [swissprot;acc:q03154]	53174	44377.4	1.19822
	Rooted	brain protein 44. [swissprot;acc:o95563]	113.374	123.463	1.08899
525	Measured	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [swissprot;acc:p30301]	10639.8	12117.3	1.13887
	Ranked	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]	215.237	230.07	1.06891
	Squared	carboxypeptidase a1 precursor (ec 3.4.17.1). [swissprot;acc:p15085]	53174	44377.4	1.19822
	Rooted	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	113.374	123.463	1.08899
526	Measured	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	10639.9	12117.4	1.13886
	Ranked	nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [swissprot;acc:p56182]	250.538	234.401	1.06884
	Squared	electron transfer flavoprotein beta-subunit (beta-etf). [swissprot;acc:p38117]	31189.6	37352.8	1.1976
	Rooted	septin 6. [swissprot;acc:q14141]	113.169	123.23	1.0889
527	Measured	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688]	4775.11	5438.18	1.13886
	Ranked	dead (asp-glu-ala-asp) box polypeptide 31 isoform 1; dead/dexh helicase ddx31. [refseq;acc:nm_022779]	248.56	232.579	1.06871
	Squared	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	18011.9	21552.8	1.19659
	Rooted	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	153.191	166.771	1.08865
528	Measured	aquaporin-chip (water channel protein for red blood cells and kidney proximal tubule) (aquaporin 1) (aqp-1) (urine water channel). [swissprot;acc:p29972]	10635.3	12111.4	1.13879
	Ranked	yme1-like 1 isoform 3; atp-dependent metalloprotease ftsh1 homolog. [refseq;acc:nm_014263]	222.146	237.393	1.06864
	Squared	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	10606	8868.81	1.19588
	Rooted	wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516]	66.941	72.7546	1.08685
529	Measured	mitochondrial import receptor subunit tom20 homolog (mitochondrial 20 kda outer membrane protein) (outer mitochondrial membrane receptor tom20). [swissprot;acc:q15388]	8600.02	9792.49	1.13866
	Ranked	atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	251.653	235.506	1.06856
	Squared	sodium-dependent multivitamin transporter (na(+)-dependent multivitamin transporter). [swissprot;acc:q9y289]	28990.9	34656.4	1.19542
	Rooted	nucleolar protein nop56 (nucleolar protein 5a). [swissprot;acc:o00567]	50.3239	54.6658	1.08628
530	Measured	peroxisomal farnesylated protein (33 kda housekeeping protein) (peroxin 19). [swissprot;acc:p40855]	8600.02	9792.49	1.13866
	Ranked	u6 snrna-associated sm-like protein lsm6 (sm protein f). [swissprot;acc:q9y4y8]	227.483	212.994	1.06803
	Squared	monoglyceride lipase; lysophospholipase-like. [refseq;acc:nm_007283]	27179.5	32490.8	1.19542
	Rooted	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	50.6537	46.6413	1.08603
531	Measured	transcription initiation factor iib (general transcription factor tfiib) (s300-ii). [swissprot;acc:q00403]	4651.88	5296.78	1.13863
	Ranked	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	223.356	209.149	1.06793
	Squared	solute carrier family 5 (iodide transporter), member 8; apical iodide transporter. [refseq;acc:nm_145913]	28980.7	34643.6	1.1954
	Rooted	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	50.6537	46.6413	1.08603
532	Measured	thyroid receptor interacting protein 3 (trip-3) (fragment). [swissprot;acc:q15649]	4651.88	5296.78	1.13863
	Ranked	zinc finger-like protein 9. [refseq;acc:nm_033414]	250.942	235.004	1.06782
	Squared	kidney and liver proline oxidase 1. [refseq;acc:nm_021232]	28967	34626.4	1.19537
	Rooted	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236]	107.961	117.197	1.08555
533	Measured	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]	4651.88	5296.78	1.13863

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.