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.


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 [...,...].
Gene description Rank Network Comparison Type Value Type Interaction Map red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1908 to 1957 of 3228 in total 
Network Comparison Type	Divided
Value Type	Ranked
Interaction Map	High confidence
Filtered	1

description	Rank	red	green	network_comparison	
ny-ren-62 antigen (fragment). [source:sptrembl;acc:q9y590]	1205	224.805	219.251	1.02533	
o-sialoglycoprotein endopeptidase. [source:refseq;acc:nm_017807]	1717	221.058	218.164	1.01327	
odd-skipped related 1; odz (odd oz/ten-m) related 1. [source:refseq;acc:nm_145260]	184	274.027	237.79	1.15239	
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [source:swissprot;acc:q16348]	224	185.969	165.623	1.12285	
oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [source:swissprot;acc:p46059]	251	186.172	166.661	1.11707	
oligophrenin 1. [source:swissprot;acc:o60890]	504	238.704	255.68	1.07112	
oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [source:swissprot;acc:q9una1]	502	238.704	255.68	1.07112	
oligoribonuclease, mitochondrial precursor (ec 3.1.-.-) (small fragment nuclease) (cgi-114). [source:swissprot;acc:q9y3b8]	1966	211.633	213.703	1.00978	
oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [source:swissprot;acc:p46977]	255	200.691	179.88	1.11569	
opioid binding protein/cell adhesion molecule precursor (obcam) (opioid-binding cell adhesion molecule) (opcml). [source:swissprot;acc:q14982]	1492	224.159	220.017	1.01883	
opsin 4 (melanopsin). [source:swissprot;acc:q9uhm6]	583	237.28	252.492	1.06411	
origin recognition complex subunit 2. [source:swissprot;acc:q13416]	3047	0.00001	0.00001	1	
origin recognition complex subunit 5. [source:swissprot;acc:o43913]	2851	0.00001	0.00001	1	
ornithine aminotransferase, mitochondrial precursor (ec 2.6.1.13) (ornithine--oxo-acid aminotransferase). [source:swissprot;acc:p04181]	1746	219.423	222.215	1.01272	
ornithine carbamoyltransferase, mitochondrial precursor (ec 2.1.3.3) (otcase) (ornithine transcarbamylase). [source:swissprot;acc:p00480]	1933	215.667	217.82	1.00998	
ornithine decarboxylase (ec 4.1.1.17) (odc). [source:swissprot;acc:p11926]	2063	207.638	205.923	1.00833	
ornithine decarboxylase antizyme inhibitor. [source:swissprot;acc:o14977]	2052	207.667	205.95	1.00834	
ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [source:swissprot;acc:q96a70]	2054	207.665	205.948	1.00834	
orphan nuclear receptor hmr (early response protein nak1) (tr3 orphan receptor). [source:swissprot;acc:p22736]	2133	207.74	206.305	1.00696	
orphan nuclear receptor nr2e1 (nuclear receptor tlx) (tailless homolog) (tll) (htll). [source:swissprot;acc:q9y466]	1544	219.762	216.081	1.01704	
orphan nuclear receptor nr5a2 (alpha-1-fetoprotein transcription factor) (hepatocytic transcription factor) (b1-binding factor) (hb1f) (cyp7a promoter binding factor). [source:swissprot;acc:o00482]	3042	0.00001	0.00001	1	
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [source:swissprot;acc:q15406]	1406	212.833	208.456	1.021	
orphan nuclear receptor nurr1 (immediate-early response protein not) (transcriptionally inducible nuclear receptor). [source:swissprot;acc:p43354]	2141	207.765	206.343	1.00689	
orphan nuclear receptor tr2. [source:swissprot;acc:p13056]	1545	219.76	216.083	1.01702	
osteoclast stimulating factor 1. [source:swissprot;acc:q92882]	759	231.809	243.289	1.04952	
ovarian carcinoma immunoreactive antigen. [source:refseq;acc:nm_017830]	2136	221.248	222.788	1.00696	
oxidation resistance 1. [source:refseq;acc:nm_181354]	2051	218.79	216.981	1.00834	
oxysterols receptor lxr-alpha (liver x receptor alpha) (nuclear orphan receptor lxr-alpha). [source:swissprot;acc:q13133]	2422	218.2	218.984	1.00359	
oxysterols receptor lxr-beta (liver x receptor beta) (nuclear orphan receptor lxr-beta) (ubiquitously-expressed nuclear receptor) (nuclear receptor ner). [source:swissprot;acc:p55055]	2416	218.2	218.984	1.00359	
p protein (melanocyte-specific transporter protein). [source:swissprot;acc:q04671]	1308	218.44	213.439	1.02343	
p10-binding protein. [source:refseq;acc:nm_024491]	1611	221.313	217.877	1.01577	
p28 ing5. [source:refseq;acc:nm_032329]	1917	215.848	218.039	1.01015	
p29ing4; candidate tumor suppressor p33 ing1 homolog. [source:refseq;acc:nm_016162]	2542	218.068	217.633	1.002	
p300/cbp-associated factor (ec 2.3.1.-) (p/caf) (histone acetylase pcaf). [source:swissprot;acc:q92831]	2733	202.229	202.172	1.00028	
p47 protein isoform a. [source:refseq;acc:nm_016143]	2201	213.642	212.254	1.00654	
p53-related protein kinase (ec 2.7.1.-) (nori-2). [source:swissprot;acc:q96s44]	2752	221.7	221.716	1.00007	
p66 alpha. [source:refseq;acc:nm_017660]	1560	167.687	170.455	1.01651	
paired box protein pax-6 (oculorhombin) (aniridia, type ii protein). [source:swissprot;acc:p26367]	1844	214.773	212.417	1.01109	
pak1 interacting protein 1; pak1-interacting protein; pak/plc-interacting protein 1. [source:refseq;acc:nm_017906]	3072	0.00001	0.00001	1	
pallidin; pallid (mouse) homolog, pallidin. [source:refseq;acc:nm_012388]	213	210.693	186.95	1.127	
palmitoyl-protein thioesterase 1 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 1). [source:swissprot;acc:p50897]	807	212.386	221.785	1.04425	
palmitoyl-protein thioesterase 2 precursor (ec 3.1.2.22) (palmitoyl- protein hydrolase 2) (ppt-2) (g14). [source:swissprot;acc:q9umr5]	199	242.735	276.059	1.13729	
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [source:swissprot;acc:q8te04]	24	58	44	1.31818	
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [source:swissprot;acc:q9bz23]	25	58	44	1.31818	
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [source:swissprot;acc:q9h999]	26	58	44	1.31818	
pantothenate kinase 4 (ec 2.7.1.33) (pantothenic acid kinase 4) (hpank4). [source:swissprot;acc:q9nve7]	2883	0.00001	0.00001	1	
parafibromin. [source:refseq;acc:nm_024529]	917	239.704	230.991	1.03772	
paraspeckle protein 1. [source:refseq;acc:nm_018282]	2533	190.417	190.824	1.00214	
parkinson disease (autosomal recessive, juvenile) 2, parkin isoform 1; parkin. [source:refseq;acc:nm_004562]	830	231.734	222.222	1.0428	
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [source:swissprot;acc:q9byg4]	965	211.987	204.964	1.03426	

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/