MK5 Microarray Data

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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 3964 to 4013 of 29840 in total

Interaction Map  : High confidence

Rank	description	Value Type	Network Comparison Type	Filtered	red	green	network_comparison
248	poly (adp-ribose) glycohydrolase. [refseq;acc:nm_003631]	Ranked	Subtracted	0	10899.4	9878.1	1021.3
	proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824]	Measured		1	13241.4	11864	1377.4
	proto-oncogene c-crk (p38) (adapter molecule crk). [swissprot;acc:p46108]		Divided		6417.18	7859.6	1.22477
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Rooted			56.0466	63.4808	1.13264
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	Squared		0	42556.5	33335.4	1.27662
249	cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661]		Subtracted	1	51616.7	42588.9	9027.8
	estradiol 17 beta-dehydrogenase 1 (ec 1.1.1.62) (17-beta-hsd 1) (placental 17-beta-hydroxysteroid dehydrogenase) (20 alpha- hydroxysteroid dehydrogenase) (20-alpha-hsd) (e2dh). [swissprot;acc:p14061]	Measured		0	2323.8	2452.23	128.43
	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	Squared	Divided		35446.2	27772	1.27633
	glycogen phosphorylase, muscle form (ec 2.4.1.1) (myophosphorylase). [swissprot;acc:p11217]			1	8875.01	6768.05	1.31131
	hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934]	Rooted		0	23.5797	26.096	1.10671
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Measured			1225.08	1079.37	1.135
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Ranked	Subtracted		10552.2	11566.4	1014.2
	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]		Divided		10551.6	11573.7	1.09687
	neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90]	Rooted	Subtracted	1	27.9136	37.2872	9.3736
	ns1-associated protein 1. [refseq;acc:nm_006372]	Ranked	Divided		237.302	212.41	1.11719
	rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427]	Squared	Subtracted	0	299.137	144.414	154.723
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Measured		1	4405.4	5782.08	1376.68
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Ranked			226.109	202.333	23.776
	transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994]	Rooted	Divided		55.5965	62.9349	1.13199
	tyrosine-protein kinase abl2 (ec 2.7.1.112) (tyrosine kinase arg). [swissprot;acc:p42684]	Measured			6417.18	7859.59	1.22477
	zinc finger protein 232. [swissprot;acc:q9uny5]	Rooted	Subtracted	0	17.1325	14.7869	2.3456
250	c-terminal binding protein 2 (ctbp2). [swissprot;acc:p56545]	Squared	Divided	1	69201.8	53013.4	1.30536
	chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557]	Rooted	Subtracted		27.9136	37.2872	9.3736
	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]	Squared		0	410.662	561.35	150.688
	dc11 protein. [refseq;acc:nm_020186]	Rooted	Divided		23.5797	26.096	1.10671
	disks large-associated protein 2 (dap-2) (sap90/psd-95-associated protein 2) (sapap2) (psd-95/sap90 binding protein 2) (fragment). [swissprot;acc:q9p1a6]	Squared			504.762	643.571	1.275
	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Ranked		1	237.302	212.41	1.11719
	histidyl-trna synthetase homolog (ec 6.1.1.21) (histidine--trna ligase homolog) (hisrs). [swissprot;acc:p49590]	Squared	Subtracted		34527.9	43507.9	8980
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Ranked	Divided	0	10551.6	11573.7	1.09687
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Measured			1225.08	1079.37	1.135
	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	Rooted		1	55.5965	62.9349	1.13199
	pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388]	Ranked	Subtracted		210.693	186.95	23.743
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]			0	12522.7	13514.5	991.8
	proto-oncogene tyrosine-protein kinase src (ec 2.7.1.112) (p60-src) (c-src). [swissprot;acc:p12931]	Measured	Divided	1	6417.18	7859.6	1.22477
	ptd016 protein. [refseq;acc:nm_016125]		Subtracted	0	30	158	128
	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]			1	4578.09	5939.91	1361.82
	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	Rooted		0	17.1341	14.7892	2.3449
251	40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174]		Divided		21.3142	23.5833	1.10646
	40s ribosomal protein s20. [swissprot;acc:p17075]	Ranked	Subtracted	1	243.5	267.21	23.71
	5,6-dihydroxyindole-2-carboxylic acid oxidase precursor (ec 1.14.18.-) (dhica oxidase) (tyrosinase-related protein 1) (trp-1) (trp1) (trp) (catalase b) (glycoprotein-75) (melanoma antigen gp75). [swissprot;acc:p17643]	Measured		0	270.264	142.417	127.847
	b-cell cll/lymphoma 6, member b (zinc finger protein); zinc finger protein 62. [refseq;acc:nm_181844]	Squared	Divided	1	69165.6	52992.1	1.30521
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		Subtracted	0	351.996	499.177	147.181
	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Measured		1	4579.34	5940.64	1361.3
	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	Rooted			27.9136	37.2872	9.3736
	histidyl-trna synthetase (ec 6.1.1.21) (histidine--trna ligase) (hisrs). [swissprot;acc:p12081]	Squared			34506.3	43476	8969.7
	ischemia/reperfusion inducible protein. [refseq;acc:nm_024640]	Ranked		0	12463.5	11482.6	980.9
	keratin associated protein 4-10; keratin associated protein 4.10. [refseq;acc:nm_033060]		Divided		10551.6	11573.6	1.09686
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Measured			1225.08	1079.38	1.13498
	max protein. [swissprot;acc:p25912]	Rooted		1	56.3054	63.7148	1.13159
	oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059]	Ranked			186.172	166.661	1.11707

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.