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	Network Comparison Type	Value Type	Interaction Map	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 951 to 1000 of 3730 in total

Network Comparison Type  : Divided
Value Type  : Ranked
Interaction Map  : High confidence

Rank	description	Filtered	red	network_comparison	green
476	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	0	8403	1.00888	8329
	potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	1	226.681	1.07527	210.814
477	saccharomyces cerevisiae nip7p homolog. [refseq;acc:nm_016101]		251.926	1.0741	234.547
	ubiquitin-conjugating enzyme e2-17 kda 3 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (e2(17)kb 3). [swissprot;acc:p47986]	0	15920	1.00886	15780.2
478	3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110]		10156.4	1.00854	10243.1
	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	1	228.051	1.07409	212.321
479	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	0	15155.8	1.00826	15031.7
	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	1	228.051	1.07409	212.321
480	neuropilin- and tolloid-like protein 2 precursor. [refseq;acc:nm_018092]		237.109	1.07405	254.667
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	0	15155.8	1.00826	15031.7
481	neuropilin- and tolloid-like protein 1 isoform 3 precursor. [refseq;acc:nm_138966]	1	237.109	1.07405	254.667
	uridine kinase-like 1. [swissprot;acc:q9nwz5]	0	11554.3	1.00802	11462.4
482	heterogenous nuclear ribonucleoprotein u (hnrnp u) (scaffold attachment factor a) (saf-a). [swissprot;acc:q00839]	1	237.109	1.07405	254.667
	kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8]	0	6156.33	1.00801	6205.67
483	runt-related transcription factor 2 (core-binding factor, alpha 1 subunit) (cbf-alpha 1) (acute myeloid leukemia 3 protein) (oncogene aml-3) (polyomavirus enhancer binding protein 2 alpha a subunit) (pebp2-alpha a) (pea2-alpha a) (sl3-3 enhancer factor 1 alpha a subunit) (sl3/akv core-binding factor alpha a subunit) (osteoblast- specific transcription factor 2) (osf-2). [swissprot;acc:q13950]	1	237.109	1.07405	254.667
	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]	0	12223.8	1.00794	12127.5
484	e1b-55kda-associated protein 5 isoform a. [refseq;acc:nm_007040]	1	237.109	1.07405	254.667
	protein c20orf45 (cgi-107). [swissprot;acc:q9y3b1]	0	11489.7	1.00661	11414.3
485	60s ribosomal protein l18. [swissprot;acc:q07020]	1	237.109	1.07405	254.667
	pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790]	0	12461.5	1.00648	12542.3
486	huntingtin interacting protein c. [refseq;acc:nm_012272]		13372.4	1.00633	13288.3
	mct-1 protein. [refseq;acc:nm_014060]	1	226.313	1.07387	243.03
487	mitochondrial ribosomal protein l22. [refseq;acc:nm_014180]
	survival motor neuron protein (component of gems 1) (gemin1). [swissprot;acc:q16637]	0	13236.8	1.00589	13159.3
488	heat shock factor binding protein 1. [swissprot;acc:o75506]		15204.2	1.00505	15127.8
	squamous cell carcinoma antigen recognized by t cells 1; u4/u6.u5 tri-snrnp-associated 110 kda protein; ige autoantigen; sart1(259) protein; sart1(800) protein. [refseq;acc:nm_005146]	1	225.026	1.07258	209.798
489	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	0	8854.04	1.00487	8811.09
	protein phosphatase 2c beta isoform (ec 3.1.3.16) (pp2c-beta). [swissprot;acc:o75688]	1	231.276	1.07257	215.627
490	dna-directed rna polymerase i 16 kda polypeptide (ec 2.7.7.6) (rpa16). [swissprot;acc:q9y2s0]	0	10388.7	1.00484	10338.7
	rho guanine nucleotide exchange factor 7 (pak-interacting exchange factor beta) (beta-pix) (cool-1) (p85). [swissprot;acc:q14155]	1	220.183	1.0719	236.015
491	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [swissprot;acc:q9bze4]		251.83	1.07184	234.951
	rwd domain containing 1; ptd013 protein; cgi-24 protein. [refseq;acc:nm_015952]	0	21970	1.00411	21880
492	serine/threonine-protein kinase pak 2 (ec 2.7.1.-) (p21-activated kinase 2) (pak-2) (pak65) (gamma-pak) (s6/h4 kinase). [swissprot;acc:q13177]	1	220.171	1.0718	235.979
	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	0	6802.96	1.00394	6829.74
493	conserved oligomeric golgi complex subunit 5 (13s golgi transport complex 90 kda subunit) (gtc-90) (golgi transport complex 1). [swissprot;acc:q9up83]	1	220.172	1.0718	235.98
	dj470l14.3 (novel protein similar to the arp2/3 protein complex subunit p21-arc (arc21)). [sptrembl;acc:q9h5b6]	0	11999.1	1.00355	12041.7
494	serine/threonine-protein kinase pak 1 (ec 2.7.1.-) (p21-activated kinase 1) (pak-1) (p65-pak) (alpha-pak). [swissprot;acc:q13153]	1	220.172	1.0718	235.98
	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	0	11985.5	1.00218	11959.4
495	26s proteasome non-atpase regulatory subunit 12 (26s proteasome regulatory subunit p55). [swissprot;acc:o00232]		11725.2	1.00195	11748.1
	serine/threonine-protein kinase pak 3 (ec 2.7.1.-) (p21-activated kinase 3) (pak-3) (beta-pak) (oligophrenin-3). [swissprot;acc:o75914]	1	220.171	1.0718	235.979
496	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]		250.938	1.07177	234.134
	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]	0	9394	1.00186	9411.49
497	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	1	251.344	1.07177	234.514
	sh2 domain binding protein 1; tpr-containing, sh2-binding phosphoprotein. [refseq;acc:nm_014633]	0	13692.7	1.00186	13718.2
498	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]		10231.8	1.00161	10248.3
	rho guanine nucleotide exchange factor 6 (pak-interacting exchange factor alpha) (alpha-pix) (cool-2). [swissprot;acc:q15052]	1	220.161	1.07172	235.95
499	inosine-5'-monophosphate dehydrogenase 2 (ec 1.1.1.205) (imp dehydrogenase 2) (impdh-ii) (impd 2). [swissprot;acc:p12268]	0	9080.73	1.00123	9069.58
	triosephosphate isomerase (ec 5.3.1.1) (tim). [swissprot;acc:p00938]	1	231.496	1.0715	248.048
500	huntingtin interacting protein e; huntingtin interactor protein e. [refseq;acc:nm_007076]	0	394	1	394
	inhibitor of growth family, member 1-like; inhibitor of growth 1-like. [refseq;acc:nm_001564]	1	224.662	1.07127	240.673

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.