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	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 551 to 600 of 3228 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence
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]	739	6434.78	5768.32	1.11554
cellular repressor of e1a-stimulated genes 2. [refseq;acc:nm_153836]	623	7013.19	6228.39	1.126
cellular repressor of e1a-stimulated genes. [refseq;acc:nm_003851]	629
centaurin beta 1 (cnt-b1). [swissprot;acc:q15027]	2123	6301.76	5977.03	1.05433
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	6000.03	5701.81	1.0523
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	7971.27	8186.02	1.02694
centromere/kinetochore protein zw10 homolog. [swissprot;acc:o43264]	3167	0.00001	0.00001	1
cerebral cell adhesion molecule. [refseq;acc:nm_016174]	1747	10241.9	9596.59	1.06724
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	900	4279.17	4713.58	1.10152
cgi-142; hepatoma-derived growth factor 2. [refseq;acc:nm_016073]	384	5279.4	4533.74	1.16447
cgthba protein (-14 gene protein). [swissprot;acc:q12980]	2562	5187.78	5291.65	1.02002
channel associated protein of synapse-110 (chapsyn-110) (discs, large homolog 2). [swissprot;acc:q15700]	2085	6159.4	5835.4	1.05552
chaperone-activity of bc1 complex-like, mitochondrial precursor (chaperone-abc1-like). [swissprot;acc:q8ni60]	1173	6305.95	5799.35	1.08735
choline dehydrogenase. [refseq;acc:nm_018397]	1556	6302.76	5875.75	1.07267
choline o-acetyltransferase (ec 2.3.1.6) (choactase) (choline acetylase) (chat). [swissprot;acc:p28329]	1139	6303.95	5790.66	1.08864
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	3375.34	3591.95	1.06417
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	3093.78	2554.89	1.21092
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	5578.02	4869.15	1.14558
chromatin-specific transcription elongation factor large subunit. [refseq;acc:nm_007192]	958	4917.77	4483.26	1.09692
chromobox protein homolog 1 (heterochromatin protein 1 homolog beta) (hp1 beta) (modifier 1 protein) (m31) (heterochromatin protein p25). [swissprot;acc:p23197]	2598	7417.58	7538.48	1.0163
chromobox protein homolog 3 (heterochromatin protein 1 homolog gamma) (hp1 gamma) (modifier 2 protein) (hech). [swissprot;acc:q13185]	2591	7422.01	7550.12	1.01726
chromobox protein homolog 5 (heterochromatin protein 1 homolog alpha) (hp1 alpha) (antigen p25). [swissprot;acc:p45973]	2590	7422.68	7551.88	1.01741
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	52	1390.33	779.167	1.78438
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	7576.84	7101.15	1.06699
chromodomain y-like protein 2. [refseq;acc:nm_152342]	1755	7577.75	7101.7	1.06703
chromosome 11 open reading frame2; chromosome 11 open reading frame2. [refseq;acc:nm_013265]	2214	6199.28	5910.12	1.04893
chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	274	2579.49	3119.98	1.20953
cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830]	837	4492.98	4063.64	1.10565
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]	2291	6048.89	5783.71	1.04585
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	7741.14	7780.98	1.00515
clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	2189	5033.55	5285.03	1.04996
clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	2197	5036.39	5285.79	1.04952
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	20431.7	24896.4	1.21852
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	6162.98	5763.25	1.06936
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	6149.86	5732.83	1.07274
cleavage and polyadenylation specificity factor, 100 kda subunit (cpsf 100 kda subunit) (fragment). [swissprot;acc:q9p2i0]	268	20127.8	24473.9	1.21593
cleavage and polyadenylation specificity factor, 160 kda subunit (cpsf 160 kda subunit). [swissprot;acc:q10570]	266	20369.9	24806.9	1.21782
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6]	288	19380.3	23422.4	1.20857
cleavage stimulation factor subunit 3; cleavage stimulation factor, 3' pre-rna, subunit 3, 77kd. [refseq;acc:nm_001326]	294	18702.6	22515.5	1.20387
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]	552	13572.8	15427.2	1.13663
cleft lip and palate associated transmembrane protein 1. [refseq;acc:nm_001294]	2337	5350.78	5123.89	1.04428

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.