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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 868 to 917 of 3228 in total

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

Rank	network_comparison	description	red	green
868	1.10322	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770]	5595.65	6173.23
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	1.10313	protein bap28. [swissprot;acc:q9h583]	3956.25	4364.25
872	1.1031	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	7480.15
873	1.1028	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [swissprot;acc:o14737]	4749.52	5237.77
874	1.10278	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [refseq;acc:nm_138793]	9921.43	10941.2
875	1.10277	steroid hormone receptor err2 (estrogen-related receptor, beta) (err-beta) (estrogen receptor-like 2) (err beta-2). [swissprot;acc:o95718]	10263.8	11318.6
876	1.10249	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	5644.68	6223.23
877	1.10243	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [swissprot;acc:q9ui95]	5797.88	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	peptide chain release factor 1, mitochondrial precursor (mrf-1). [swissprot;acc:o75570]	5166.04	5694.55
881	1.10229	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	5912.84	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	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [swissprot;acc:o75352]	5167.15	5695.44
885	1.10219	mitochondrial translational release factor 1-like. [refseq;acc:nm_019041]	5168.01	5696.12
886	1.10217	upstream binding protein 1 (lbp-1a). [refseq;acc:nm_014517]	5903.18	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	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
891	1.10188	lymphoid enhancer binding factor 1 (lef-1) (t cell-specific transcription factor 1-alpha) (tcf1-alpha). [swissprot;acc:q9uju2]	5385.04	5933.65
892	1.10182	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333]	6784.67	7475.48
893	1.10171	e-1 enzyme. [refseq;acc:nm_021204]	6603.09	7274.72
894	1.1016	parafibromin. [refseq;acc:nm_024529]	4331.17	4771.22
895		heterogeneous nuclear ribonucleoprotein l (hnrnp l). [swissprot;acc:p14866]	10247.8	11289
896	1.10155	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [swissprot;acc:p08240]	5208.27	5737.17
897	1.10153	histone deacetylase 2 (hd2). [swissprot;acc:q92769]	5929.48	6531.48
898	1.10152	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
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	1.10151	histone deacetylase 1 (hd1). [swissprot;acc:q13547]	5929.61	6531.55
902	1.10147	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	10246.1	11285.8
903	1.10146	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
904	1.10031	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [swissprot;acc:o00410]	6167.33	6785.98
905	1.1003	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [swissprot;acc:p11474]	10230.1	11256.2
906	1.10023	ran-gtp binding protein (fragment). [sptrembl;acc:o60518]	6165.1	6783.01
907	1.10019	ba305p22.3 (breast carcinoma amplified sequence 4). [sptrembl;acc:q8ndy6]	11852.9	10773.5
908	1.10014	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [refseq;acc:nm_152414]	11848.8	10770.3
909	1.10005	kinesin family member c3. [refseq;acc:nm_005550]	5995.49	6595.35
910	1.09999	sipl protein. [refseq;acc:nm_018269]	6522.94	7175.18
911	1.09996	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [swissprot;acc:q99471]	4982.81	5480.91
912		prefoldin subunit 6 (protein ke2). [swissprot;acc:o15212]
913	1.09943	ww domain binding protein 2 (wbp-2). [swissprot;acc:q969t9]	5768.5	6342.05
914	1.09942	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [swissprot;acc:p07858]	6513.45	7161
915	1.09893	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	6289.72	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]

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.