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	Gene	Interaction Map	Network Comparison Type	Filtered	red	network_comparison	green

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Showing element 551 to 600 of 3228 in total

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

description	Rank	red	network_comparison	green
cell division protein kinase 9 (ec 2.7.1.-) (serine/threonine-protein kinase pitalre) (c-2k). [swissprot;acc:p50750]	2974	0.00001	1	0.00001
cellular modulator of immune recognition. [refseq;acc:nm_145021]	739	5768.32	1.11554	6434.78
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	623	6228.39	1.126	7013.19
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]	629
centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]	2123	5977.03	1.05433	6301.76
centaurin beta 2 (cnt-b2). [swissprot;acc:q15057]	2122
centaurin beta 5 (cnt-b5). [swissprot;acc:q96p50]	2121
centaurin gamma 1. [swissprot;acc:q99490]	2157	5701.81	1.0523	6000.03
centaurin gamma 2. [swissprot;acc:q9upq3]	2155
centaurin gamma 3. [swissprot;acc:q96p47]	2158
centromere protein j; centrosomal p4.1-associated protein; lyst-interacting protein lip1; lag-3-associated protein. [refseq;acc:nm_018451]	2499	8186.02	1.02694	7971.27
centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264]	3167	0.00001	1	0.00001
cerebral cell adhesion molecule. [refseq;acc:nm_016174]	1747	9596.59	1.06724	10241.9
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	900	4713.58	1.10152	4279.17
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	384	4533.74	1.16447	5279.4
cgthba protein (-14 gene protein). [swissprot;acc:q12980]	2562	5291.65	1.02002	5187.78
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	2085	5835.4	1.05552	6159.4
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	1173	5799.35	1.08735	6305.95
choline dehydrogenase. [refseq;acc:nm_018397]	1556	5875.75	1.07267	6302.76
choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]	1139	5790.66	1.08864	6303.95
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585]	1840	3591.95	1.06417	3375.34
cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3]	1846
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	271	2554.89	1.21092	3093.78
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]	468	4869.15	1.14558	5578.02
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]	958	4483.26	1.09692	4917.77
chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197]	2598	7538.48	1.0163	7417.58
chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185]	2591	7550.12	1.01726	7422.01
chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973]	2590	7551.88	1.01741	7422.68
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	52	779.167	1.78438	1390.33
chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873]	47
chromodomain protein, y chromosome-like isoform a; cdy-like, autosomal; testis-specific chromodomain y-like protein. [refseq;acc:nm_004824]	1758	7101.15	1.06699	7576.84
chromodomain y-like protein 2. [refseq;acc:nm_152342]	1755	7101.7	1.06703	7577.75
chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]	2214	5910.12	1.04893	6199.28
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	274	3119.98	1.20953	2579.49
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	837	4063.64	1.10565	4492.98
cisplatin resistance related protein crr9p. [refseq;acc:nm_030782]	3197	0.00001	1	0.00001
clathrin coat assembly protein ap180 (clathrin coat associated protein ap180) (91 kda synaptosomal-associated protein). [swissprot;acc:o60641]	2291	5783.71	1.04585	6048.89
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]	2675	7780.98	1.00515	7741.14
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	2189	5285.03	1.04996	5033.55
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	2197	5285.79	1.04952	5036.39
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]	262	24896.4	1.21852	20431.7
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]	1678	5763.25	1.06936	6162.98
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]	1551	5732.83	1.07274	6149.86
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	268	24473.9	1.21593	20127.8
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	266	24806.9	1.21782	20369.9
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	288	23422.4	1.20857	19380.3
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	294	22515.5	1.20387	18702.6
cleavage stimulation factor, 50 kda subunit (cstf 50 kda subunit) (cf-1 50 kda subunit). [swissprot;acc:q05048]	3129	0.00001	1	0.00001
cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	552	15427.2	1.13663	13572.8
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]	2337	5123.89	1.04428	5350.78

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.