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	Gene	red	Value Type	Rank	green	Interaction Map	description	Filtered	network_comparison

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Showing element 3101 to 3150 of 3228 in total

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

red	Rank	green	description	network_comparison
11852.9	907	10773.5	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	1.10019
12365.2	307	14824.9	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	1.19892
12471.7	378	14561.7	hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0]	1.16758
12503.3	748	11212	ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812]	1.11517
12515.4	744	11221.1	cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857]	1.11535
12780.7	363	10876.4	cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	1.17509
12786.6	362	10879.9	g2/mitotic-specific cyclin b1. [swissprot;acc:p14635]	1.17525
12787.6	361	10880.5	cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	1.17528
12796.8	360	10886	g2/mitotic-specific cyclin b2. [swissprot;acc:o95067]	1.17553
12798.9	359	10887.2	cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	1.17559
12839	353	10911.1	p66 alpha. [refseq;acc:nm_017660]	1.17669
	354		transcription repressor p66 beta component of the mecp1 complex. [refseq;acc:nm_020699]
	355		tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [swissprot;acc:p17735]
12998.5	380	15138.2	acyl-coa dehydrogenase, very-long-chain specific, mitochondrial precursor (ec 1.3.99.-) (vlcad). [swissprot;acc:p49748]	1.16461
13241.4	731	11864	methyltransferase like 2. [refseq;acc:nm_018396]	1.1161
	732		cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763]
	733		fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263]
	734		proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]
13261.9	295	11017.8	ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	1.20368
13680.5	306	11409.6	pnas-18. [sptrembl;acc:q9bzu3]	1.19903
13768.2	301	11466	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	1.20078
14021.4	267	11523	ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	1.21682
14229.2	346	16780.7	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6]	1.17931
14830.5	554	13050.3	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	1.13641
14924.4	334	17655.2	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]	1.18298
14976.4	607	13246.6	likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235]	1.13058
15182.5	503	13277.9	tumor suppressor p53-binding protein 2 (p53-binding protein 2) (53bp2) (bcl2-binding protein) (bbp). [swissprot;acc:q13625]	1.14344
15213.4	601	13418.1	symplekin. [swissprot;acc:q92797]	1.1338
15274.9	490	13346.9	protein phosphatase 1, regulatory (inhibitor) subunit 13b; apoptosis-stimulating protein of p53, 1. [refseq;acc:nm_015316]	1.14445
15427.2	552	13572.8	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	1.13663
15959.9	330	18957.1	septin 6. [swissprot;acc:q14141]	1.1878
15999.1	328	19007.1	brain protein 44. [swissprot;acc:o95563]	1.18801
	329		septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]
16067.4	327	19094.4	septin 10 isoform 1. [refseq;acc:nm_144710]	1.18839
16069.8	219	12885.6	transforming protein n-ras. [swissprot;acc:p01111]	1.24711
16070.4	218	12886	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	1.24712
16071.6	216	12886.8	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	1.24714
	217		ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]
16074	215	12888.4	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	1.24717
16177.9	325	19235.4	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	1.18899
16771.5	145	12889.1	ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395]	1.30122
17385.9	376	14889.2	44050 protein. [refseq;acc:nm_178832]	1.16769
	377		nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [swissprot;acc:q12972]
17396.9	350	20483.9	sedlin. [swissprot;acc:o14582]	1.17745
	351		synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296]
	352		bet3 homolog. [swissprot;acc:o43617]
17710.9	198	13977.7	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	1.26708
17738.5	195	13995.6	cyclin g1 (cyclin g). [swissprot;acc:p51959]	1.26743
	196	13995.7	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	1.26742
	197		serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]

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.