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

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Showing element 551 to 600 of 3228 in total

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

description	Rank	green	red	network_comparison
cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750]	2974	0.00001	0.00001	1
cellular modulator of immune recognition. [refseq;acc:nm_145021]	1179	212.672	218.186	1.02593
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	699	209.118	220.438	1.05413
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]	705
centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]	2037	220.812	218.919	1.00865
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	218.452	220.659	1.0101
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	202.105	206.773	1.0231
centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264]	3167	0.00001	0.00001	1
cerebral cell adhesion molecule. [refseq;acc:nm_016174]	2508	193.871	194.349	1.00247
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	172	205.556	174.667	1.17685
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	832	222.222	231.734	1.0428
cgthba protein (-14 gene protein). [swissprot;acc:q12980]	644	230.596	217.67	1.05938
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	2657	216.7	216.934	1.00108
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	1730	212.567	215.336	1.01303
choline dehydrogenase. [refseq;acc:nm_018397]	1647	214.149	217.256	1.01451
choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]	1967	213.702	211.632	1.00978
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	267.352	241.373	1.10763
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	256.835	287.41	1.11905
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	228.297	252.39	1.10553
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]	902	228.762	237.62	1.03872
chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197]	2535	188.63	188.228	1.00214
chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185]	2509	188.366	187.902	1.00247
chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973]	2505	188.326	187.853	1.00252
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	335	284	312	1.09859
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	330
chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]	2553	193.467	193.12	1.0018
chromodomain y-like protein 2. [refseq;acc:nm_152342]	2556	193.46	193.119	1.00177
chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]	1211	219.759	214.364	1.02517
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	153	298.263	249.663	1.19466
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	982	235.351	243.312	1.03383
cisplatin resistance related protein crr9p. [refseq;acc:nm_030782]	3197	0.00001	0.00001	1
clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641]	1392	213.876	218.471	1.02148
clathrin coat assembly protein ap50 (clathrin coat associated protein ap50) (plasma membrane adaptor ap-2 50 kda protein) (ha2 50 kda subunit) (clathrin assembly protein complex 2 medium chain) (ap-2 mu 2 chain). [swissprot;acc:p20172]	2208	200.413	199.129	1.00645
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	399	226.226	207.889	1.08821
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	405	226.209	207.931	1.0879
cleavage and polyadenylation specific factor 4, 30kd subunit; cleavage-polyadenylation specificity factor, 30kd; no arches-like (zebrafish) zinc finger protein; cleavage-polyadenylation specificity factor. [refseq;acc:nm_006693]	850	112.329	107.842	1.04161
cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006]	1657	216.195	219.314	1.01443
cleavage and polyadenylation specific factor 6, 68 kd subunit; pre-mrna cleavage factor im (68kd); cleavage and polyadenylation specific factor 6, 68kd subunit; pre-mrna cleavage factor i, 68kd subunit. [refseq;acc:nm_007007]	1480	214.55	218.664	1.01918
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	871	114.552	110.2	1.03949
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	854	112.772	108.289	1.0414
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	1006	120.375	116.524	1.03305
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	1089	125.004	121.428	1.02945
cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048]	3129	0.00001	0.00001	1
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	2140	162.665	161.547	1.00692
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]	756	235.583	224.434	1.04968

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.