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

Results: HTML CSV LaTeX

Showing element 6408 to 6457 of 77072 in total

Value Type

: Measured
Interaction Map

: High confidence
Filtered

: 1

green	Network Comparison Type	Rank	red	description	network_comparison
6220.45	Subtracted	1004	5680.76	lysosomal acid lipase/cholesteryl ester hydrolase precursor (ec 3.1.1.13) (lal) (acid cholesteryl ester hydrolase) (sterol esterase) (lipase a) (cholesteryl esterase). [swissprot;acc:p38571]	539.69
		1005		seryl-trna synthetase, mitochondrial precursor (ec 6.1.1.11) (serine--trna ligase) (serrsmt). [swissprot;acc:q9np81]
		1006		seryl-trna synthetase (ec 6.1.1.11) (serine--trna ligase) (serrs). [swissprot;acc:p49591]
6221.72	Divided	1479	5787.03	hepatocyte nuclear factor 3-alpha (hnf-3a) (forkhead box protein a1). [swissprot;acc:p55317]	1.07511
6221.72	Subtracted	1518	5787.03		434.69
6222.04	Divided	560	5480.24	cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	1.13536
		561		transforming protein rhoc (h9). [swissprot;acc:p08134]
		562		thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
		563		3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
		564		transforming protein rhoa (h12). [swissprot;acc:p06749]
	Subtracted	612		cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520]	741.8
		613		transforming protein rhoc (h9). [swissprot;acc:p08134]
		614		thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762]
		615		3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
		616		transforming protein rhoa (h12). [swissprot;acc:p06749]
6223.23	Divided	876	5644.68	peroxisomal carnitine octanoyltransferase (ec 2.3.1.-) (cot). [swissprot;acc:q9ukg9]	1.10249
6223.23	Subtracted	877	5644.68		578.55
6226.13	Divided	1220	5735.65	cyclin m3; ancient conserved domain protein 3. [refseq;acc:nm_017623]	1.08551
6226.13	Subtracted	1219	5735.65		490.48
6226.23	Divided	1222	5735.74	cyclin m1; ancient conserved domain protein 1. [refseq;acc:nm_020348]	1.08551
6226.23	Subtracted	1218	5735.74		490.49
6226.46	Divided	1219	5735.95	tcd37 homolog; prune. [refseq;acc:nm_021222]	1.08552
6226.46	Subtracted	1217	5735.95	tcd37 homolog; prune. [refseq;acc:nm_021222]	490.51
6226.52	Divided	1218	5736	cyclin m4; ancient conserved domain protein 4. [refseq;acc:nm_020184]	1.08552
6226.52	Subtracted	1216	5736		490.52
6226.88	Divided	1221	5736.34	cyclin m2; ancient conserved domain protein 2. [refseq;acc:nm_017649]	1.08551
6226.88	Subtracted	1215	5736.34		490.54
6227.33	Divided	1789	5839.72	serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4]	1.06637
		1790		kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241]
		1791		serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9]
		1792		serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965]
		1793		cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]
	Subtracted	1767		serine/threonine protein kinase 12 (ec 2.7.1.37) (aurora- and ipl1- like midbody-associated protein 1) (aim-1) (aurora/ipl1-related kinase 2) (aurora-related kinase 2) (stk-1) (aurora-b). [swissprot;acc:q96gd4]	387.61
		1768		kinesin-like protein kif23 (mitotic kinesin-like protein-1) (kinesin- like protein 5). [swissprot;acc:q02241]
		1769		serine/threonine protein kinase 13 (ec 2.7.1.37) (aurora/ipl1/eg2 protein 2) (aurora/ipl1-related kinase 3) (aurora-c). [swissprot;acc:q9uqb9]
		1770		serine/threonine kinase 6 (ec 2.7.1.37) (serine/threonine kinase 15) (aurora/ipl1-related kinase 1) (aurora-related kinase 1) (hark1) (aurora-a) (breast-tumor-amplified kinase). [swissprot;acc:o14965]
		1771		cylindromatosis (turban tumor syndrome); cylindromatosis 1, turban tumor syndrome. [refseq;acc:nm_015247]
6230.55	Divided	1499	5798.31	hepatocyte nuclear factor 3-beta (hnf-3b) (forkhead box protein a2). [swissprot;acc:q9y261]	1.07455
6230.55	Subtracted	1544	5798.31		432.24
6232.83	Divided	1260	5754.84	rad54-like protein; rad54 homolog. [refseq;acc:nm_003579]	1.08306
6232.83	Subtracted	1272	5754.84	rad54-like protein; rad54 homolog. [refseq;acc:nm_003579]	477.99
6233.12	Divided	397	5367.04	nuclear protein skip (ski-interacting protein) (snw1 protein) (nuclear receptor coactivator ncoa-62). [swissprot;acc:q13573]	1.16137
6233.12	Subtracted	470	5367.04		866.08
6233.52	Divided	721	5580.97	syntaxin 7. [swissprot;acc:o15400]	1.11692
6233.52	Subtracted	740	5580.97	syntaxin 7. [swissprot;acc:o15400]	652.55
6236.53	Divided	1731	5840.77	lamin b2. [swissprot;acc:q03252]	1.06776
6236.53	Subtracted	1734	5840.77	lamin b2. [swissprot;acc:q03252]	395.76
6237.19	Divided	2452	6042.36	succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040]	1.03224
6237.19	Subtracted	2387	6042.36		194.83
6239.55	Divided	1569	5819.37	traf and tnf receptor-associated protein; ets1-associated protein 2. [refseq;acc:nm_016614]	1.0722

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.

- http://analysis.yellowcouch.org/