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

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

Results: HTML CSV LaTeX

Showing element 883 to 932 of 3228 in total

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

Rank	description	red	green	network_comparison	
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	
908	basic helix-loop-helix domain containing, class b, 5; trinucleotide repeat containing 20. [source:refseq;acc:nm_152414]	11848.8	10770.3	1.10014	
909	kinesin family member c3. [source:refseq;acc:nm_005550]	5995.49	6595.35	1.10005	
910	sipl protein. [source:refseq;acc:nm_018269]	6522.94	7175.18	1.09999	
911	prefoldin subunit 5 (c-myc binding protein mm-1) (myc modulator 1). [source:swissprot;acc:q99471]	4982.81	5480.91	1.09996	
912	prefoldin subunit 6 (protein ke2). [source:swissprot;acc:o15212]	4982.81	5480.91	1.09996	
913	ww domain binding protein 2 (wbp-2). [source:swissprot;acc:q969t9]	5768.5	6342.05	1.09943	
914	cathepsin b precursor (ec 3.4.22.1) (cathepsin b1) (app secretase). [source:swissprot;acc:p07858]	6513.45	7161	1.09942	
915	cytochrome b5 reductase b5r.2. [source:refseq;acc:nm_016229]	6289.72	6911.96	1.09893	
916	cytochrome b5 reductase 1 (b5r.1). [source:refseq;acc:nm_016243]	6289.72	6911.96	1.09893	
917	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [source:swissprot;acc:p00387]	6289.72	6911.96	1.09893	
918	scratch; scratch 1. [source:refseq;acc:nm_031309]	7281.6	8001.64	1.09888	
919	limbic system-associated membrane protein precursor (lsamp). [source: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). [source:sptrembl;acc:q9nq03]	7273.78	7991.72	1.0987	
921	translation initiation factor if-2, mitochondrial precursor (if-2mt) (if-2(mt)). [source:swissprot;acc:p46199]	6324.31	6948.5	1.0987	
922	tubulin-tyrosine ligase. [source:refseq;acc:nm_153712]	5511.2	6054.71	1.09862	
923	eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [source:swissprot;acc:q99613]	4057.54	4457.66	1.09861	
924	opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [source:swissprot;acc:q14982]	5406.5	5939.42	1.09857	
925	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 1, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 1). [source:swissprot;acc:q15118]	5637.43	6193.07	1.09856	
926	[pyruvate dehydrogenase [lipoamide]] kinase isozyme 2, mitochondrial precursor (ec 2.7.1.99) (pyruvate dehydrogenase kinase isoform 2). [source:swissprot;acc:q15119]	5637.45	6193.08	1.09856	
927	dipeptidylpeptidase 10; dipeptidyl peptidase iv-related protein 3. [source:refseq;acc:nm_020868]	5638.64	6194.22	1.09853	
928	cytochrome c oxidase assembly protein cox11, mitochondrial precursor. [source:swissprot;acc:q9y6n1]	5638.46	6194.04	1.09853	
929	surfeit locus protein 1. [source:swissprot;acc:q15526]	5638.46	6194.04	1.09853	
930	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [source:swissprot;acc:p42658]	5638.65	6194.23	1.09853	
931	seprase (ec 3.4.21.-) (fibroblast activation protein alpha) (integral membrane serine protease) (170-kda melanoma membrane-bound gelatinase). [source:swissprot;acc:q12884]	5638.59	6194.17	1.09853	
932	cox15 homolog isoform 2 precursor; cytochrome c oxidase subunit 15; cytochrome c oxidase assembly protein. [source:refseq;acc:nm_004376]	5638.46	6194.04	1.09853	

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/