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

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Showing element 862 to 911 of 3228 in total

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

Rank	green	description	red	network_comparison
862	4497.74	probable ribosome biogenesis protein nep1 (c2f protein). [swissprot;acc:q92979]	4076.72	1.10327
863	6173.23	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [swissprot;acc:p56730]	5595.65	1.10322
864		ring finger protein 44. [refseq;acc:nm_014901]
865		phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [swissprot;acc:p27986]
866		ring finger protein 38. [refseq;acc:nm_022781]
867		phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [swissprot;acc:q92569]
868		sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]
869		atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576]
870		phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459]
871	4364.25	protein bap28. [swissprot;acc:q9h583]	3956.25	1.10313
872	7480.15	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668]	6781.05	1.1031
873	5237.77	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	4749.52	1.1028
874	10941.2	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	9921.43	1.10278
875	11318.6	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	10263.8	1.10277
876	6223.23	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	5644.68	1.10249
877	6391.75	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	5797.88	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	5694.55	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	5166.04	1.1023
881	6517.69	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	5912.84	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	5695.44	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	5167.15	1.10224
885	5696.12	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	5168.01	1.10219
886	6506.32	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	5903.18	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	5896.82	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775]	5350.87	1.10203
891	5933.65	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	5385.04	1.10188
892	7475.48	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	6784.67	1.10182
893	7274.72	e-1 enzyme. [refseq;acc:nm_021204]	6603.09	1.10171
894	4771.22	parafibromin. [refseq;acc:nm_024529]	4331.17	1.1016
895	11289	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	10247.8
896	5737.17	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	5208.27	1.10155
897	6531.48	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	5929.48	1.10153
898	6531.52	multiple coagulation factor deficiency 2; neural stem cell derived neuronal survival protein; multiple coagulation factor deficiency protein 2. [refseq;acc:nm_139279]	5929.55	1.10152
899		dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [sptrembl;acc:q9ujn8]
900	4279.17	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902]	4713.58
901	6531.55	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	5929.61	1.10151
902	11285.8	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	10246.1	1.10147
903	5492.51	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	1.10146
904	6785.98	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410]	6167.33	1.10031
905	11256.2	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	10230.1	1.1003
906	6783.01	ran-gtp binding protein (fragment). [sptrembl;acc:o60518]	6165.1	1.10023
907	10773.5	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	11852.9	1.10019
908	10770.3	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	11848.8	1.10014
909	6595.35	kinesin family member c3. [refseq;acc:nm_005550]	5995.49	1.10005
910	7175.18	sipl protein. [refseq;acc:nm_018269]	6522.94	1.09999
911	5480.91	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	4982.81	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.