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	red	green	network_comparison

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Showing element 2051 to 2100 of 3228 in total

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

description	Rank	red	green	network_comparison
polybromo 1. [refseq;acc:nm_018165]	2052	5634.8	5952.7	1.05642
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]	2579	4979.44	5071.53	1.01849
polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947]	2809	0.00001	0.00001	1
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	283	5221.28	6314.35	1.20935
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999]	765	4726.38	5258.95	1.11268
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	2583	3926.4	3857.88	1.01776
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	2630	3985.17	3928.38	1.01446
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863]	1156	5840.77	6355.89	1.08819
polymyositis/scleroderma autoantigen 2 (autoantigen pm/scl 2) (polymyositis/scleroderma autoantigen 100 kda) (pm/scl-100) (p100 polymyositis-scleroderma overlap syndrome associated autoantigen). [swissprot;acc:q01780]	2531	6141.97	6291.08	1.02428
polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481]	2097	6024.47	6356.56	1.05512
polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	2611	6380.6	6476.18	1.01498
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	2613
polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]	2281	5783.73	6048.91	1.04585
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]	2293	5783.76	6048.94
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	448	6259.3	7190.91	1.14884
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]	1202	4913.07	5337.95	1.08648
possible global transcription activator snf2l1. [swissprot;acc:p28370]	2055	5634.8	5952.7	1.05642
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]	2057
possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]	2054
postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171]	3034	0.00001	0.00001	1
potassium channel modulatory factor 1; potassium channel modulatory factor; differentially expressed in branching tubulogenesis 91; zinc finger, zz domain containing 1. [refseq;acc:nm_020122]	1816	5633.44	5997	1.06454
potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121]	2975	0.00001	0.00001	1
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	139	2759.61	2099.49	1.31442
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	2188	6682.7	7018.29	1.05022
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	2176	6674.58	7015.93	1.05114
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	2196	6688.64	7020.02	1.04954
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	91	2416.53	1700.8	1.42082
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	88	2411.93	1695.45	1.42259
potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980]	90	2414.77	1698.75	1.4215
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	720	6593.17	7364.55	1.117
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	716
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]	1349	6153.36	6640.77	1.07921
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	1453	5602.01	6031.05	1.07659
pp1201 protein. [refseq;acc:nm_022152]	709	5317.78	5944.25	1.11781
pp3111 protein. [refseq;acc:nm_022156]	1964	4374.32	4126.96	1.05994
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	2559	5291.65	5187.78	1.02002
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245]	2473	7765.3	8004	1.03074
pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424]	2466
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425]	2472
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426]	2467
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	554	14830.5	13050.3	1.13641
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	331	20287.2	17083.8	1.18751
pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811]	1942	5805.06	6158.16	1.06083
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	304	4855.46	5824.52	1.19958
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	368	5082.66	5959.99	1.17261
prefoldin subunit 1. [swissprot;acc:o60925]	1554	5875.75	6302.76	1.07267
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9]	1073	5207.39	5687.2	1.09214
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	1072
prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4]	3130	0.00001	0.00001	1
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	911	4982.81	5480.91	1.09996

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.