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	description	Rank	Filtered	Interaction Map	network_comparison	red	green

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Showing element 527 to 576 of 3228 in total

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

description	Rank	network_comparison	red	green
ccaat displacement protein (cdp) (cut-like 1). [swissprot;acc:p39880]	556	1.06638	207.27	194.368
ccaat-binding transcription factor subunit b (cbf-b) (nf-y protein chain a) (nf-ya) (caat-box dna binding protein subunit a). [swissprot;acc:p23511]	36	1.27519	260.532	204.309
ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	408	1.08649	255.112	234.804
ccr4-not transcription complex, subunit 3; not3 (negative regulator of transcription 3, yeast) homolog. [refseq;acc:nm_014516]	3163	1	0.00001	0.00001
ccr4-not transcription complex, subunit 4; not4 (negative regulator of transcription 4, yeast) homolog; ccr4-not transcription complex, subunit. [refseq;acc:nm_013316]	1390	1.02148	218.47	213.875
ccr4-not transcription complex, subunit 6-like. [refseq;acc:nm_144571]	2958	1	0.00001	0.00001
ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1]	3226
ccr4-not transcription complex, subunit 8 (caf1-like protein) (califp). [swissprot;acc:q9uff9]	2890
cd109; gov system alloantigens on platelets. [refseq;acc:nm_133493]	2075	1.00803	221.703	223.483
cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	418	1.08417	233.539	253.197
cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	420
cda11 protein. [refseq;acc:nm_032026]	1579	1.01644	213.181	209.732
cdc42 guanine exchange factor 9; hpem-2 collybistin. [refseq;acc:nm_015185]	1778	1.0121	216.878	214.286
cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	437	1.07878	209.921	226.459
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]	692	1.05532	217.602	206.195
cdk-activating kinase assembly factor mat1 (ring finger protein mat1) (menage a trois) (cdk7/cyclin h assembly factor) (p36) (p35) (cyclin g1 interacting protein). [swissprot;acc:p51948]	3209	1	0.00001	0.00001
cdp-diacylglycerol--inositol 3-phosphatidyltransferase (ec 2.7.8.11) (phosphatidylinositol synthase) (ptdins synthase) (pi synthase). [swissprot;acc:o14735]	2155	1.00681	200.063	198.71
cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	2739	1.00022	198.278	198.321
cell division control protein 2 homolog (ec 2.7.1.-) (p34 protein kinase) (cyclin-dependent kinase 1) (cdk1). [swissprot;acc:p06493]	1585	1.01631	168.145	170.888
cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661]	1481	1.01915	208.432	204.516
cell division protein kinase 2 (ec 2.7.1.-) (p33 protein kinase). [swissprot;acc:p24941]	1583	1.01634	168.091	170.837
cell division protein kinase 3 (ec 2.7.1.-). [swissprot;acc:q00526]	1581	1.01637	168.002	170.753
cell division protein kinase 5 (ec 2.7.1.-) (tau protein kinase ii catalytic subunit) (tpkii catalytic subunit) (serine/threonine protein kinase pssalre). [swissprot;acc:q00535]	2850	1	0.00001	0.00001
cell division protein kinase 8 (ec 2.7.1.-) (protein kinase k35). [swissprot;acc:p49336]	2990
cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750]	2974
cellular modulator of immune recognition. [refseq;acc:nm_145021]	1179	1.02593	218.186	212.672
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	699	1.05413	220.438	209.118
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]	705
centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]	2037	1.00865	218.919	220.812
centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]	2035
centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]	2034
centaurin gamma 1. [swissprot;acc:q99490]	1924	1.0101	220.659	218.452
centaurin gamma 2. [swissprot;acc:q9upq3]	1922
centaurin gamma 3. [swissprot;acc:q96p47]	1925
centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451]	1317	1.0231	206.773	202.105
centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264]	3167	1	0.00001	0.00001
cerebral cell adhesion molecule. [refseq;acc:nm_016174]	2508	1.00247	194.349	193.871
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	172	1.17685	174.667	205.556
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	832	1.0428	231.734	222.222
cgthba protein (-14 gene protein). [swissprot;acc:q12980]	644	1.05938	217.67	230.596
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	2657	1.00108	216.934	216.7
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	1730	1.01303	215.336	212.567
choline dehydrogenase. [refseq;acc:nm_018397]	1647	1.01451	217.256	214.149
choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]	1967	1.00978	211.632	213.702
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	269	1.10763	241.373	267.352
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]	275
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	234	1.11905	287.41	256.835
chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028]	282	1.10553	252.39	228.297
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]	902	1.03872	237.62	228.762
chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197]	2535	1.00214	188.228	188.63

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.