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

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Showing element 401 to 450 of 3730 in total

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

description	Rank	Filtered	red	green	network_comparison
atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705]	1658	1	217.925	214.826	1.01443
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	241		227.357	254.15	1.11785
atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]	1655		219.062	215.942	1.01445
atp synthase coupling factor 6, mitochondrial precursor (ec 3.6.3.14) (f6). [swissprot;acc:p18859]	2893		0.00001	0.00001	1
atp synthase coupling factor b, mitochondrial precursor. [swissprot;acc:q99766]	2022		208.601	210.464	1.00893
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049]	1687		215.345	212.386	1.01393
atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]	2644		194.097	194.328	1.00119
atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964]	2834		0.00001	0.00001	1
atp synthase gamma chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p36542]	1563		218.277	214.739	1.01648
atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]	456		210.225	226.578	1.07779
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]	1564		218.277	214.739	1.01648
atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450]	2209		199.129	200.413	1.00645
atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288]	2166		215.925	214.481	1.00673
atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396]	2689		213.792	213.619	1.00081
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	224	0	9815.6	8889.93	1.10413
	1871	1	222.819	225.228	1.01081
atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]	426	0	9412.67	9676.67	1.02805
	2727	1	221.001	220.927	1.00033
atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010]	2728
atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762]	1703		216.079	219.024	1.01363
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	529		251.653	235.506	1.06856
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	328		258.437	235.183	1.09888
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	428		253.852	234.808	1.0811
atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	990		243.297	235.373	1.03367
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]	1365		228.644	223.736	1.02194
atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]	1126		218.487	212.656	1.02742
atpase, h+ transporting, lysosomal v0 subunit a isoform 4; vacuolar proton pump 116 kda accessory subunit; vacuolar proton pump, subunit 2; h(+)-transporting two-sector atpase, noncatalytic accessory protein 1b; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 1b; renal tubular acidosis; atpase, h+ transporting, lysosomal (vacuolar proton pump) non-catalytic accessory protein 2 (38kd). [refseq;acc:nm_020632]	1120		218.528	212.676	1.02752
atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]	1384		218.471	213.876	1.02148
atrophin-1 interacting protein 1; activin receptor interacting protein 1; likely ortholog of mouse activin receptor interacting protein 1; atrophin-1 interacting protein a; membrane associated guanylate kinase 2; activin receptor interacting p. [refseq;acc:nm_012301]	1035		221.682	228.68	1.03157
au rna-binding protein/enoyl-coenzyme a hydratase precursor; au rna-binding protein/enoyl-coenzyme a hydratase; 3-methylglutaconyl-coa hydratase; mga type i. [refseq;acc:nm_001698]	2913		0.00001	0.00001	1
autoantigen ngp-1. [swissprot;acc:q13823]	670		250.302	236.817	1.05694
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	1729		187.582	190.028	1.01304
autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	1540		240.077	236.015	1.01721
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	2003		208.315	206.41	1.00923
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	1559		196.191	192.996	1.01655
b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]	2655		201.445	201.667	1.0011
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	1556		196.192	192.996	1.01656
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	980		130.289	134.713	1.03396
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	181		229.818	267.265	1.16294
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	244		227.357	254.15	1.11785
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	464		210.578	226.764	1.07686
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1]	3117		0.00001	0.00001	1
ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	2599		211.662	211.361	1.00142
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	307	0	1091	1021	1.06856
	2148	1	217.871	219.366	1.00686
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]	2115		214.632	213.14	1.007
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	931		159.13	164.917	1.03637
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	452		224.161	207.972	1.07784
	464	0	10076.4	9928.08	1.01494
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	24		13730.5	8257	1.66289

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.