Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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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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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 858 to 907 of 3228 in total 
Value Type	Measured
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	red	green	network_comparison	
858	n-deacetylase/n-sulfotransferase 4. [source:refseq;acc:nm_022569]	5210.58	5749.33	1.1034	
859	heparan sulfate n-deacetylase/n-sulfotransferase (ec 2.8.2.8) (n-hsst) (hsnst) ([heparan sulfate]-glucosamine n-sulfotransferase) (n-heparan sulfate sulfotransferase) (glucosaminyl n-deacetylase/n- sulfotransferase). [source:swissprot;acc:p52848]	5210.58	5749.33	1.1034	
860	protein cdc27hs (cell division cycle protein 27 homolog) (h-nuc). [source:swissprot;acc:p30260]	5210.58	5749.33	1.1034	
861	bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [source:swissprot;acc:p54132]	5734.15	6326.41	1.10329	
862	probable ribosome biogenesis protein nep1 (c2f protein). [source:swissprot;acc:q92979]	4076.72	4497.74	1.10327	
863	neurotrypsin precursor (ec 3.4.21.-) (motopsin) (leydin). [source:swissprot;acc:p56730]	5595.65	6173.23	1.10322	
864	ring finger protein 44. [source:refseq;acc:nm_014901]	5595.65	6173.23	1.10322	
865	phosphatidylinositol 3-kinase regulatory alpha subunit (pi3-kinase p85-alpha subunit) (ptdins-3-kinase p85-alpha) (pi3k). [source:swissprot;acc:p27986]	5595.65	6173.23	1.10322	
866	ring finger protein 38. [source:refseq;acc:nm_022781]	5595.65	6173.23	1.10322	
867	phosphatidylinositol 3-kinase regulatory gamma subunit (pi3-kinase p85-gamma subunit) (ptdins-3-kinase p85-gamma) (p55pik). [source:swissprot;acc:q92569]	5595.65	6173.23	1.10322	
868	sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [source:swissprot;acc:q12770]	5595.65	6173.23	1.10322	
869	atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p06576]	5595.65	6173.23	1.10322	
870	phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [source:swissprot;acc:o00459]	5595.65	6173.23	1.10322	
871	protein bap28. [source:swissprot;acc:q9h583]	3956.25	4364.25	1.10313	
872	epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [source:swissprot;acc:q15668]	6781.05	7480.15	1.1031	
873	programmed cell death protein 5 (tfar19 protein) (tf-1 cell apoptosis related gene-19 protein). [source:swissprot;acc:o14737]	4749.52	5237.77	1.1028	
874	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source: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). [source:swissprot;acc:o95718]	10263.8	11318.6	1.10277	
876	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [source:swissprot;acc:q9ukg9]	5644.68	6223.23	1.10249	
877	mitotic spindle assembly checkpoint protein mad2b (mad2-like 2) (hrev7). [source:swissprot;acc:q9ui95]	5797.88	6391.75	1.10243	
878	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	5797.88	6391.75	1.10243	
879	nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [source:swissprot;acc:q99567]	5797.88	6391.75	1.10243	
880	peptide chain release factor 1, mitochondrial precursor (mrf-1). [source:swissprot;acc:o75570]	5166.04	5694.55	1.1023	
881	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [source: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). [source:swissprot;acc:p12953]	5912.84	6517.69	1.10229	
883	adp-ribosylation factor-like protein 4. [source:swissprot;acc:p40617]	5912.84	6517.69	1.10229	
884	mannose-p-dolichol utilization defect 1 protein (suppressor of lec15 and lec35 glycosylation mutation homolog) (sl15). [source:swissprot;acc:o75352]	5167.15	5695.44	1.10224	
885	mitochondrial translational release factor 1-like. [source:refseq;acc:nm_019041]	5168.01	5696.12	1.10219	
886	upstream binding protein 1 (lbp-1a). [source:refseq;acc:nm_014517]	5903.18	6506.32	1.10217	
887	transcription factor cp2; transcription factor cp2, alpha globin. [source:refseq;acc:nm_005653]	5903.18	6506.32	1.10217	
888	lbp-9. [source:refseq;acc:nm_014553]	5903.18	6506.32	1.10217	
889	splicing factor, arginine/serine-rich 3 (pre-mrna splicing factor srp20) (x16 protein). [source:swissprot;acc:p23152]	5903.18	6506.32	1.10217	
890	tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [source: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). [source:swissprot;acc:q9uju2]	5385.04	5933.65	1.10188	
892	cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [source:swissprot;acc:p16333]	6784.67	7475.48	1.10182	
893	e-1 enzyme. [source:refseq;acc:nm_021204]	6603.09	7274.72	1.10171	
894	parafibromin. [source:refseq;acc:nm_024529]	4331.17	4771.22	1.1016	
895	heterogeneous nuclear ribonucleoprotein l (hnrnp l). [source:swissprot;acc:p14866]	10247.8	11289	1.1016	
896	signal recognition particle receptor alpha subunit (sr-alpha) (docking protein alpha) (dp-alpha). [source:swissprot;acc:p08240]	5208.27	5737.17	1.10155	
897	histone deacetylase 2 (hd2). [source: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. [source:refseq;acc:nm_139279]	5929.55	6531.52	1.10152	
899	dj153g14.2 (possible ca binding protein similar to nefa) (fragment). [source:sptrembl;acc:q9ujn8]	5929.55	6531.52	1.10152	
900	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902]	4713.58	4279.17	1.10152	
901	histone deacetylase 1 (hd1). [source:swissprot;acc:q13547]	5929.61	6531.55	1.10151	
902	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [source: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). [source:swissprot;acc:p24666]	4986.58	5492.51	1.10146	
904	importin beta-3 subunit (karyopherin beta-3 subunit) (ran-binding protein 5). [source:swissprot;acc:o00410]	6167.33	6785.98	1.10031	
905	steroid hormone receptor err1 (estrogen-related receptor, alpha) (err-alpha) (estrogen receptor-like 1). [source:swissprot;acc:p11474]	10230.1	11256.2	1.1003	
906	ran-gtp binding protein (fragment). [source:sptrembl;acc:o60518]	6165.1	6783.01	1.10023	
907	ba305p22.3 (breast carcinoma amplified sequence 4). [source:sptrembl;acc:q8ndy6]	11852.9	10773.5	1.10019	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/