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

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Showing element 875 to 924 of 3228 in total

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

Rank	network_comparison	red	description	green
875	1.10277	10263.8	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	11318.6
876	1.10249	5644.68	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	6223.23
877	1.10243	5797.88	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	6391.75
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	1.1023	5166.04	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	5694.55
881	1.10229	5912.84	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	6517.69
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	1.10224	5167.15	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	5695.44
885	1.10219	5168.01	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	5696.12
886	1.10217	5903.18	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	6506.32
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	1.10203	5350.87	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775]	5896.82
891	1.10188	5385.04	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	5933.65
892	1.10182	6784.67	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	7475.48
893	1.10171	6603.09	e-1 enzyme. [refseq;acc:nm_021204]	7274.72
894	1.1016	4331.17	parafibromin. [refseq;acc:nm_024529]	4771.22
895		10247.8	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	11289
896	1.10155	5208.27	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	5737.17
897	1.10153	5929.48	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	6531.48
898	1.10152	5929.55	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]	6531.52
899			dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]
900		4713.58	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	4279.17
901	1.10151	5929.61	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	6531.55
902	1.10147	10246.1	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	11285.8
903	1.10146	4986.58	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]	5492.51
904	1.10031	6167.33	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410]	6785.98
905	1.1003	10230.1	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	11256.2
906	1.10023	6165.1	ran-gtp binding protein (fragment). [sptrembl;acc:o60518]	6783.01
907	1.10019	11852.9	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	10773.5
908	1.10014	11848.8	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	10770.3
909	1.10005	5995.49	kinesin family member c3. [refseq;acc:nm_005550]	6595.35
910	1.09999	6522.94	sipl protein. [refseq;acc:nm_018269]	7175.18
911	1.09996	4982.81	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	5480.91
912			prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
913	1.09943	5768.5	ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9]	6342.05
914	1.09942	6513.45	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	7161
915	1.09893	6289.72	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	6911.96
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	1.09888	7281.6	scratch; scratch 1. [refseq;acc:nm_031309]	8001.64
919	1.09878	5396.36	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	5929.41
920	1.0987	7273.78	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	7991.72
921		6324.31	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [swissprot;acc:p46199]	6948.5
922	1.09862	5511.2	tubulin-tyrosine ligase. [refseq;acc:nm_153712]	6054.71
923	1.09861	4057.54	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613]	4457.66
924	1.09857	5406.5	opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [swissprot;acc:q14982]	5939.42

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.