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

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Showing element 401 to 450 of 3730 in total

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

description	Rank	Filtered	green	red	network_comparison
atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705]	834	1	6218.77	5623.18	1.10592
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	1970		4126.96	4374.32	1.05994
atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]	869		6173.23	5595.65	1.10322
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]	1507		6610.46	6152.78	1.07439
atp synthase delta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p30049]	811		6655.11	6000.07	1.10917
atp synthase f chain, mitochondrial (ec 3.6.3.14). [swissprot;acc:p56134]	2036		7315.59	6920.71	1.05706
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]	824		6263.02	5657.53	1.10702
atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691]	1657		5131.89	5488.7	1.06953
atp synthase oligomycin sensitivity conferral protein, mitochondrial precursor (ec 3.6.3.14) (oscp). [swissprot;acc:p48047]	825		6263.02	5657.53	1.10702
atp-binding cassette, sub-family c, member 10; multidrug resistance-associated protein 7. [refseq;acc:nm_033450]	2676		7741.14	7780.98	1.00515
atp-binding cassette, sub-family d, member 3 (70 kda peroxisomal membrane protein) (pmp70). [swissprot;acc:p28288]	1380		6555.41	6079.46	1.07829
atp-citrate synthase (ec 2.3.3.8) (atp-citrate (pro-s-)-lyase) (citrate cleavage enzyme). [swissprot;acc:p53396]	2005		6421.65	6064.92	1.05882
atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	377	0	931.405	884.254	1.05332
	1574	1	5472.96	5106.13	1.07184
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]	100	0	402	594	1.47761
	1838	1	6108.72	5739.49	1.06433
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]	1839
atp-dependent dna helicase q5 (recq protein-like 5) (recq5). [swissprot;acc:o94762]	1552		6464.16	6025.86	1.07274
atp-dependent rna helicase ddx18 (dead-box protein 18) (myc-regulated dead-box protein) (mrdb). [swissprot;acc:q9nvp1]	463		4264.46	3720.18	1.1463
atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7]	326		4081.21	3432.96	1.18883
atp-dependent rna helicase mgc2835; atp-dependent rna helicase; apoptosis related protein apr-5; dead box helicase 97 kda. [refseq;acc:nm_024072]	392		4236.95	3641.89	1.16339
atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010]	836		4477.43	4049	1.10581
atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2]	642		5414.23	4810.85	1.12542
atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]	760		6533.39	5870.2	1.11298
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]	789		6547.99	5890.59	1.1116
atrophin-1 (dentatorubral-pallidoluysian atrophy protein). [swissprot;acc:p54259]	2283		6048.88	5783.7	1.04585
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]	2355		5492.58	5262.6	1.0437
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]	566		4274.79	3766.14	1.13506
autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	203		9352.11	11757.8	1.25723
autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	414		5815.13	6744.05	1.15974
axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645]	792		7526.2	6772.75	1.11125
b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	1633		9251.2	9899.79	1.07011
b-cell lymphoma 3-encoded protein (bcl-3 protein). [swissprot;acc:p20749]	2658		8211.05	8278.73	1.00824
b-cell lymphoma 6 protein (bcl-6) (zinc finger protein 51) (laz-3 protein) (bcl-5). [swissprot;acc:p41182]	1635		9251.16	9899.73	1.07011
b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	198		13977.7	17710.9	1.26708
b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681]	609		3438.82	3886.62	1.13022
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	1973		4126.96	4374.32	1.05994
ba138e2.1.2 (formin-binding protein 17 (fbp17), isoform 2). [sptrembl;acc:q96lh6]	1728		5127.66	5475.44	1.06782
ba203i16.1 (hypothetical protein kiaa0970). [sptrembl;acc:q9h1w1]	3117		0.00001	0.00001	1
ba207c16.2 (fragment). [sptrembl;acc:q9nql7]	2636		7108.89	7017.82	1.01298
ba271b5.1 (similar to ribosomal protein s7). [sptrembl;acc:q9h1s9]	292	0	12473	11223	1.11138
	1641	1	6186.39	5782.92	1.06977
ba304i5.1 (novel lipase) (fragment). [sptrembl;acc:q96lg2]	1000		6220.45	5680.76	1.095
ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	907		10773.5	11852.9	1.10019
ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	191	0	904.149	743.066	1.21678
	299	1	5907.12	4914.27	1.20203
ba508n22.1 (hspc025) (fragment). [sptrembl;acc:q9hcw5]	9	0	6410	85	75.4118

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.