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

Results: HTML CSV LaTeX

Showing element 2051 to 2100 of 3228 in total

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

description	Rank	network_comparison	red	green
polybromo 1. [refseq;acc:nm_018165]	2591	1.00147	220.02	219.696
polyglutamine binding protein 1; nuclear protein containing ww domain 38 kd. [refseq;acc:nm_005710]	784	1.04789	224.385	235.131
polyhomeotic like 3; early development regulator 3; polyhomeotic 3. [refseq;acc:nm_024947]	2809	1	0.00001	0.00001
polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	435	1.07909	221.522	205.286
polymerase (dna directed) sigma; topoisomerase-related function protein 4-1; polymerase (dna-directed) sigma. [refseq;acc:nm_006999]	2095	1.00763	229.266	227.53
polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467]	429	1.08064	239.709	259.038
polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468]	451	1.07785	239.092	257.705
polymerase delta-interacting protein 1; tnfaip1-like. [refseq;acc:nm_178863]	1204	1.02535	219.022	213.607
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]	953	1.03512	198.494	205.466
polypeptide n-acetylgalactosaminyltransferase 2; udp-galnac transferase 2. [refseq;acc:nm_004481]	1811	1.01168	216.854	214.35
polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	1412	1.02095	206.102	210.42
polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	1414
polypyrimidine tract binding protein 2; neural polypyrimidine tract binding protein; ptb-like protein. [refseq;acc:nm_021190]	1382	1.02148	218.47	213.876
polypyrimidine tract-binding protein 1 (ptb) (heterogeneous nuclear ribonucleoprotein i) (hnrnp i) (57 kda rna-binding protein pptb-1). [swissprot;acc:p26599]	1394			213.875
ponsin; sh3-domain protein 5 (ponsin). [refseq;acc:nm_015385]	918	1.03731	212.952	205.292
porphobilinogen deaminase (ec 4.3.1.8) (hydroxymethylbilane synthase) (hmbs) (pre-uroporphyrinogen synthase) (pbg-d). [swissprot;acc:p08397]	2708	1.0006	227.796	227.66
possible global transcription activator snf2l1. [swissprot;acc:p28370]	2594	1.00147	220.02	219.696
possible global transcription activator snf2l2 (snf2-alpha). [swissprot;acc:p51531]	2596
possible global transcription activator snf2l4 (snf2-beta) (brg-1 protein) (mitotic growth and transcription activator) (brahma protein homolog 1). [swissprot;acc:p51532]	2593
postsynaptic protein cript; hspc139 protein. [refseq;acc:nm_014171]	3034	1	0.00001	0.00001
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]	2119	1.00696	221.248	222.788
potassium channel tetramerisation domain containing 3; ny-ren-45 antigen. [refseq;acc:nm_016121]	2975	1	0.00001	0.00001
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183]	145	1.20293	265.639	319.546
potassium voltage-gated channel subfamily a member 1 (potassium channel kv1.1) (huki) (hbk1). [swissprot;acc:q09470]	475	1.07547	226.727	210.816
potassium voltage-gated channel subfamily a member 2 (potassium channel kv1.2) (rbk2) (hbk5) (ngk1) (mk2) (hukiv). [swissprot;acc:p16389]	474	1.07576	226.789	210.818
potassium voltage-gated channel subfamily a member 4 (potassium channel kv1.4) (hk1) (hpcn2) (hbk4) (hukii). [swissprot;acc:p22459]	476	1.07527	226.681	210.814
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979]	123	1.21681	269.23	327.601
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281]	120	1.21699	269.278	327.709
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]	122	1.21688	269.248	327.642
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	718	1.05402	223.121	211.685
potential carboxypeptidase-like protein x2 precursor. [swissprot;acc:q8n436]	714
potential phospholipid-transporting atpase ih (ec 3.6.3.1) (atpase class i type 11a) (atpase is). [swissprot;acc:p98196]	1843	1.01115	212.455	210.113
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	1820	1.01164	220.462	217.926
pp1201 protein. [refseq;acc:nm_022152]	1627	1.01515	217.446	214.2
pp3111 protein. [refseq;acc:nm_022156]	236	1.11785	227.357	254.15
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	641	1.05938	217.67	230.596
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245]	1787	1.01206	206.332	203.874
pre-b-cell leukemia transcription factor-1 (homeobox protein pbx1) (homeobox protein prl). [swissprot;acc:p40424]	1779
pre-b-cell leukemia transcription factor-2 (homeobox protein pbx2) (g17 protein). [swissprot;acc:p40425]	1786
pre-b-cell leukemia transcription factor-3 (homeobox protein pbx3). [swissprot;acc:p40426]	1781
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	2635	1.00132	166.612	166.393
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	1445	1.02003	134.233	136.922
pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811]	1743	1.01288	218.176	215.402
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	473	1.07637	225.661	209.651
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	594	1.06256	223.282	210.136
prefoldin subunit 1. [swissprot;acc:o60925]	1645	1.01451	217.256	214.149
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9]	1310	1.02341	226.439	221.26
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765]	1309
prefoldin subunit 4 (protein c-1). [swissprot;acc:q9nqp4]	3130	1	0.00001	0.00001
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	977	1.03402	228.953	221.421

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.