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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 2080 to 2129 of 3228 in total

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

description	Rank	red	green	network_comparison
potential carboxypeptidase x precursor (ec 3.4.17.-) (metallocarboxypeptidase cpx-1). [swissprot;acc:q96sm3]	718	223.121	211.685	1.05402
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	212.455	210.113	1.01115
potential phospholipid-transporting atpase iia (ec 3.6.1.-). [swissprot;acc:o75110]	1820	220.462	217.926	1.01164
pp1201 protein. [refseq;acc:nm_022152]	1627	217.446	214.2	1.01515
pp3111 protein. [refseq;acc:nm_022156]	236	227.357	254.15	1.11785
pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	641	217.67	230.596	1.05938
pre-b-cell leukemia transcription factor 4. [refseq;acc:nm_025245]	1787	206.332	203.874	1.01206
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	166.612	166.393	1.00132
pre-mrna cleavage complex ii protein pcf11 (fragment). [swissprot;acc:o94913]	1445	134.233	136.922	1.02003
pre-mrna cleavage factor i, 59 kda subunit. [refseq;acc:nm_024811]	1743	218.176	215.402	1.01288
pre-mrna processing factor 31 homolog; pre-mrna processing factor 31 homolog (yeast). [refseq;acc:nm_015629]	473	225.661	209.651	1.07637
pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508]	594	223.282	210.136	1.06256
prefoldin subunit 1. [swissprot;acc:o60925]	1645	217.256	214.149	1.01451
prefoldin subunit 2 (hspc231). [swissprot;acc:q9uhv9]	1310	226.439	221.26	1.02341
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	0.00001	0.00001	1
prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	977	228.953	221.421	1.03402
prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]	978
preimplantation protein 3; likely ortholog of preimplantation protein 3. [refseq;acc:nm_015387]	574	221.807	208.264	1.06503
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768]	211	285.684	252.234	1.13261
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810]	207
presenilin enhancer 2; hematopoietic stem/progenitor cells protein mds033. [refseq;acc:nm_172341]	3100	0.00001	0.00001	1
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7]	736	232.601	244.534	1.0513
presenilin-like protein 2 (ec 3.4.99.-) (sppl2a protein). [swissprot;acc:q8tct8]	734
presenilins associated rhomboid-like protein. [refseq;acc:nm_018622]	1841	212.455	210.113	1.01115
presynaptic density protein 95 (psd-95) (discs, large homolog 4) (postsynaptic density-95). [swissprot;acc:p78352]	2658	216.933	216.7	1.00108
presynaptic protein sap102 (synapse-associated protein 102) (neuroendocrine-dlg) (ne-dlg) (discs, large homolog 3). [swissprot;acc:q92796]	2659
presynaptic protein sap97 (synapse-associated protein 97) (discs, large homolog 1) (hdlg). [swissprot;acc:q12959]	2660	216.937	216.704
prip-interacting protein pipmt; prip-interacting protein with methyltransferase domain. [refseq;acc:nm_024831]	913	210.863	218.878	1.03801
prkca-binding protein (protein kinase c-alpha binding protein) (protein interacting with c kinase 1). [swissprot;acc:q9nrd5]	3143	0.00001	0.00001	1
probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	376	257.017	234.945	1.09395
probable atp-dependent helicase ddx35 (deah-box protein 35). [swissprot;acc:q9h5z1]	2645	194.097	194.328	1.00119
probable atp-dependent rna helicase ddx20 (dead-box protein 20) (dead- box protein dp 103) (component of gems 3) (gemin3). [swissprot;acc:q9uhi6]	1675	228.496	231.729	1.01415
probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	837	231.734	222.222	1.0428
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185]	1097	209.123	203.208	1.02911
probable cation-transporting atpase 1 (ec 3.6.1.-). [swissprot;acc:q9nq11]	2266	211.597	210.416	1.00561
probable dimethyladenosine transferase (ec 2.1.1.-) (s- adenosylmethionine-6-n',n'-adenosyl(rrna) dimethyltransferase) (18s rrna dimethylase). [swissprot;acc:q9unq2]	1321	226.347	221.259	1.023
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879]	1221	211.959	217.258	1.025
probable leucyl-trna synthetase, mitochondrial precursor (ec 6.1.1.4) (leucine--trna ligase) (leurs). [swissprot;acc:q15031]	1737	218.99	216.189	1.01296
probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	1031	242.978	235.518	1.03167
probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	497	251.344	234.514	1.07177
probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	989	218.462	211.345	1.03367
probable serine protease htra4 precursor (ec 3.4.21.-). [swissprot;acc:p83105]	988	218.461	211.343	1.03368
probable serine/threonine-protein kinase kiaa0537 (ec 2.7.1.-). [swissprot;acc:o60285]	727	208.873	219.71	1.05188
programmed cell death 10; apoptosis-related protein 15. [refseq;acc:nm_007217]	3052	0.00001	0.00001	1
programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	985	233.402	225.782	1.03375

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.