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

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Showing element 873 to 922 of 3228 in total

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

Rank	description	red	green	network_comparison
873	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	4749.52	5237.77	1.1028
874	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	9921.43	10941.2	1.10278
875	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	10263.8	11318.6	1.10277
876	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	5644.68	6223.23	1.10249
877	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	5797.88	6391.75	1.10243
878	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [swissprot;acc:q9y6g3]
879	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [swissprot;acc:q99567]
880	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	5166.04	5694.55	1.1023
881	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	5912.84	6517.69	1.10229
882	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase ac39 subunit) (v-atpase 40 kda accessory protein) (p39) (32 kda accessory protein). [swissprot;acc:p12953]
883	adp-ribosylation factor-like protein 4. [swissprot;acc:p40617]
884	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	5167.15	5695.44	1.10224
885	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	5168.01	5696.12	1.10219
886	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	5903.18	6506.32	1.10217
887	transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653]
888	lbp-9. [refseq;acc:nm_014553]
889	splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [swissprot;acc:p23152]
890	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775]	5350.87	5896.82	1.10203
891	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	5385.04	5933.65	1.10188
892	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	6784.67	7475.48	1.10182
893	e-1 enzyme. [refseq;acc:nm_021204]	6603.09	7274.72	1.10171
894	parafibromin. [refseq;acc:nm_024529]	4331.17	4771.22	1.1016
895	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	10247.8	11289
896	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	5208.27	5737.17	1.10155
897	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	5929.48	6531.48	1.10153
898	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]	5929.55	6531.52	1.10152
899	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]
900	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	4713.58	4279.17
901	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	5929.61	6531.55	1.10151
902	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	10246.1	11285.8	1.10147
903	red cell acid phosphatase 1, isozyme f (ec 3.1.3.2) (acp1) (low molecular weight phosphotyrosine protein phosphatase) (ec 3.1.3.48) (adipocyte acid phosphatase, isozyme alpha). [swissprot;acc:p24666]	4986.58	5492.51	1.10146
904	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410]	6167.33	6785.98	1.10031
905	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	10230.1	11256.2	1.1003
906	ran-gtp binding protein (fragment). [sptrembl;acc:o60518]	6165.1	6783.01	1.10023
907	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	11852.9	10773.5	1.10019
908	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	11848.8	10770.3	1.10014
909	kinesin family member c3. [refseq;acc:nm_005550]	5995.49	6595.35	1.10005
910	sipl protein. [refseq;acc:nm_018269]	6522.94	7175.18	1.09999
911	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	4982.81	5480.91	1.09996
912	prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
913	ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9]	5768.5	6342.05	1.09943
914	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	6513.45	7161	1.09942
915	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	6289.72	6911.96	1.09893
916	cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]
917	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]
918	scratch; scratch 1. [refseq;acc:nm_031309]	7281.6	8001.64	1.09888
919	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	5396.36	5929.41	1.09878
920	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	7273.78	7991.72	1.0987
921	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199]	6324.31	6948.5
922	tubulin-tyrosine ligase. [refseq;acc:nm_153712]	5511.2	6054.71	1.09862

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.