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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Value Type description Interaction Map Rank Network Comparison Type red Gene Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1832 to 1881 of 3228 in total 
Value Type	Measured
Interaction Map	High confidence
Network Comparison Type	Divided
Filtered	1

description	Rank	red	green	network_comparison	
nf-kappab inhibitor alpha (major histocompatibility complex enhancer- binding protein mad3) (i-kappa-b-alpha) (ikappabalpha) (ikb-alpha). [source:swissprot;acc:p25963]	2733	7913.63	7939.94	1.00332	
nf-kappab inhibitor beta (nf-kappa-bib) (i-kappa-b-beta) (ikappabbeta) (ikb-beta) (ikb-b) (thyroid receptor interacting protein 9) (tr- interacting protein 9). [source:swissprot;acc:q15653]	2660	8277.6	8210.21	1.00821	
nf-kappab inhibitor epsilon (nf-kappa-bie) (i-kappa-b-epsilon) (ikappabepsilon) (ikb-epsilon) (ikbe). [source:swissprot;acc:o00221]	2655	8290.91	8220.11	1.00861	
ngd5 protein homolog (cgi-53). [source:swissprot;acc:q9y366]	3133	0.00001	0.00001	1	
nhp2-like protein 1 (high mobility group-like nuclear protein 2 homolog 1) ([u4/u6.u5] tri-snrnp 15.5 kda protein) (otk27). [source:swissprot;acc:p55769]	533	4651.88	5296.78	1.13863	
nicotinamide nucleotide adenylyltransferase 3; pyridine nucleotide adenylyltransferase 3. [source:refseq;acc:nm_178177]	1487	5573.64	5991.58	1.07499	
nicotinate-nucleotide pyrophosphorylase [carboxylating] (ec 2.4.2.19) (quinolinate phosphoribosyltransferase [decarboxylating]) (qaprtase) (qprtase). [source:swissprot;acc:q15274]	1028	5704	6241.36	1.09421	
nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [source:swissprot;acc:q9gzt8]	936	5628.21	6180.37	1.09811	
nin one binding protein; adenocarcinoma antigen recognized by t lymphocytes 4. [source:refseq;acc:nm_014062]	1956	4689.78	4973.44	1.06048	
nipsnap1 protein. [source:swissprot;acc:q9bpw8]	2770	0.00001	0.00001	1	
nipsnap2 protein (glioblastoma amplified sequence). [source:swissprot;acc:o75323]	2918	0.00001	0.00001	1	
nitrilase 1. [source:refseq;acc:nm_005600]	1766	5829.61	6218.27	1.06667	
nitrogen fixation cluster-like. [source:refseq;acc:nm_014301]	477	9649.61	11053.5	1.14549	
nk6 transcription factor related, locus 2; nk homeobox family 6, b; glial and testis-specific homeobox protein; homeobox 6b. [source:refseq;acc:nm_177400]	2909	0.00001	0.00001	1	
nnp-1 protein (novel nuclear protein 1) (nucleolar protein nop52) (nop52) (d21s2056e). [source:swissprot;acc:p56182]	460	3790.11	4346.98	1.14693	
nonspecific lipid-transfer protein, mitochondrial precursor (nsl-tp) (sterol carrier protein 2) (scp-2) (sterol carrier protein x) (scp-x) (scpx). [source:swissprot;acc:p22307]	1363	6322.75	6820.5	1.07872	
nostrin. [source:refseq;acc:nm_052946]	496	4682.87	4093.05	1.1441	
nov protein homolog precursor (novh) (nephroblastoma overexpressed gene protein homolog). [source:swissprot;acc:p48745]	2970	0.00001	0.00001	1	
ns1-associated protein 1. [source:refseq;acc:nm_006372]	184	4069.83	5252.17	1.29051	
nuclear autoantigen sp-100 (speckled 100 kda) (nuclear dot-associated sp100 protein) (lysp100b). [source:swissprot;acc:p23497]	3184	0.00001	0.00001	1	
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	318	34190.9	40795.8	1.19318	
nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [source:refseq;acc:nm_004289]	1664	7433.73	7950.61	1.06953	
nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [source:swissprot;acc:q14494]	1663	7433.73	7950.61	1.06953	
nuclear factor nf-kappa-b p100/p49 subunits (h2tf1) (oncogene lyt-10) (lyt10) [contains: nuclear factor nf-kappa-b p52 subunit]. [source:swissprot;acc:q00653]	2661	8277.66	8210.26	1.00821	
nuclear factor nf-kappa-b p105 subunit (dna-binding factor kbf1) (ebp- 1) [contains: nuclear factor nf-kappa-b p50 subunit]. [source:swissprot;acc:p19838]	2659	8277.7	8210.29	1.00821	
nuclear factor related to kappa b binding protein. [source:refseq;acc:nm_006165]	2823	0.00001	0.00001	1	
nuclear factor, interleukin 3 regulated. [source:refseq;acc:nm_005384]	1232	5869.24	6367.8	1.08494	
nuclear fragile x mental retardation protein interacting protein 1; nuclear fragile x mental retardation intercating protein 1; nuclear fragile x mental retardation protein-interacting protein 1. [source:refseq;acc:nm_012345]	534	4651.88	5296.78	1.13863	
nuclear hormone receptor nor-1 (neuron-derived orphan receptor 1) (mitogen induced nuclear orphan receptor). [source:swissprot;acc:q92570]	1282	6230.38	6744.35	1.08249	
nuclear inhibitor of protein phosphatase-1 (nipp-1) (protein phosphatase 1, regulatory inhibitor subunit 8) [includes: activator of rna decay (ec 3.1.4.-) (ard-1)]. [source:swissprot;acc:q12972]	377	17385.9	14889.2	1.16769	
nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	333	5039.63	5961.83	1.18299	
nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [source:swissprot;acc:p35658]	3008	0.00001	0.00001	1	
nuclear pore complex protein nup88 (nucleoporin nup88) (88 kda nuclear pore complex protein). [source:swissprot;acc:q99567]	879	5797.88	6391.75	1.10243	
nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [source:swissprot;acc:p52948]	1061	5412.23	5913.4	1.0926	
nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [source:swissprot;acc:q13573]	397	5367.04	6233.12	1.16137	
nuclear protein ukp68. [source:refseq;acc:nm_024824]	106	4241.57	5810.79	1.36996	
nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [source:swissprot;acc:q9bzk7]	796	6834.54	7590.49	1.11061	
nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [source:refseq;acc:nm_181782]	2144	5859.1	6173.7	1.05369	
nuclear rna export factor 1 (tip associating protein) (tip-associated protein) (mrna export factor tap). [source:swissprot;acc:q9ubu9]	424	5207.78	6010.45	1.15413	
nuclear rna export factor 3 (tap-like protein 3) (tapl-3). [source:swissprot;acc:q9h4d5]	423	5207.03	6010.1	1.15423	
nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [source:swissprot;acc:q9h1b4]	422	5206.9	6010.04	1.15425	
nuclear transcription factor y subunit beta (nf-y protein chain b) (nf-yb) (ccaat-binding transcription factor subunit a) (cbf-a) (caat- box dna binding protein subunit b). [source:swissprot;acc:p25208]	608	4510.61	5098.74	1.13039	
nuclear transcription factor y subunit gamma (nf-y protein chain c) (nuclear factor yc) (nf-yc) (ccaat-binding transcription factor subunit c) (cbf-c) (transactivator hsm-1/2). [source:swissprot;acc:q13952]	136	3620.77	4763.34	1.31556	
nuclear transport factor 2 (ntf-2) (placental protein 15) (pp15). [source:swissprot;acc:p13662]	3113	0.00001	0.00001	1	
nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [source:swissprot;acc:p16991]	2094	6682.05	7051.02	1.05522	
nucleobindin 1 precursor (calnuc). [source:swissprot;acc:q02818]	937	5859.25	6432.03	1.09776	
nucleobindin 2 precursor (dna-binding protein nefa). [source:swissprot;acc:p80303]	939	5859.25	6432.03	1.09776	
nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	428	3721.19	4288.17	1.15237	
nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [source:swissprot;acc:q14978]	2842	0.00001	0.00001	1	
nucleolar protein family a, member 1; gar1 protein. [source:refseq;acc:nm_018983]	213	4446.72	5553.79	1.24896	

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/