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.

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

Results: HTML CSV LaTeX

Showing element 401 to 450 of 3730 in total

Value Type  : Measured
Network Comparison Type  : Divided
Interaction Map  : High confidence

Rank	description	Filtered	red	network_comparison	green
201	swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]	0	6804.88	1.1958	5690.63
	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	1	4810.22	1.26294	6075.04
202	crooked neck-like protein 1 (crooked neck homolog) (hcrn) (cgi-201) (mstp021). [swissprot;acc:q9bzj0]	0	606.049	1.19421	723.75
	enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511]	1	4812.01	1.26269	6076.09
203	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]		11757.8	1.25723	9352.11
	microtubule-interacting protein that associates with traf3; interleukin 13 receptor alpha 1-binding protein-1. [refseq;acc:nm_015650]	0	304	1.19408	363
204	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	1	4512.19	1.25339	5655.52
	ubiquitin-like protein smt3b (sentrin 2) (hsmt3). [swissprot;acc:p55855]	0	7981.68	1.19395	6685.11
205	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	1	4512.19	1.25339	5655.52
	spectrin beta chain, brain 4 (spectrin, non-erythroid beta chain 4) (beta-v spectrin) (bspecv). [swissprot;acc:q9nrc6]	0	5418.2	1.19245	4543.75
206	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	1	5720.25	1.24965	4577.5
	pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278]	0	1124.15	1.19157	943.423
207	cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747]		403.827	1.19069	339.154
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	1	4771.21	1.24946	5961.43
208	fructose-1,6-bisphosphatase isozyme 2 (ec 3.1.3.11) (d-fructose-1,6- bisphosphate 1-phosphohydrolase) (fbpase). [swissprot;acc:o00757]	0	6596.23	1.19061	5540.2
	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	1	4068.78	1.24907	5082.18
209	small nuclear ribonucleoprotein associated proteins b and b' (snrnp-b) (sm protein b/b') (sm-b/sm-b') (smb/smb'). [swissprot;acc:p14678]	0	93.5	1.18717	111
	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]	1	4068.78	1.24907	5082.18
210	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]	0	1053.33	1.18697	887.413
	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	1	4068.82	1.24906	5082.21
211	ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376]	0	2464	1.18661	2076.5
	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	1	4068.91	1.24905	5082.27
212	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]		4446.72	1.24896	5553.79
	ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966]	0	2464	1.18661	2076.5
213	arsenical pump-driving atpase (ec 3.6.3.16) (arsenite-translocating atpase) (arsenical resistance atpase) (arsenite-transporting atpase) (arsa) (asna-i). [swissprot;acc:o43681]		1162.21	1.18471	1376.88
	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]	1	4446.72	1.24896	5553.79
214	similar to zinc finger protein 277. [sptrembl;acc:q8wwa6]	0	13174.7	1.18447	15605.1
	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	1	4074.83	1.24827	5086.49
215	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]		16074	1.24717	12888.4
	zinc finger protein 277. [swissprot;acc:q9nrm2]	0	13174.7	1.18447	15605.1
216	ataxin 2; olivopontocerebellar ataxia 2, autosomal dominant. [refseq;acc:nm_002973]		12478	1.18256	14756
	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	1	16071.6	1.24714	12886.8
217	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]
	signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458]	0	903.967	1.17199	771.309
218	transforming protein p21/h-ras-1 (c-h-ras). [swissprot;acc:p01112]	1	16070.4	1.24712	12886
	tubulin gamma-1 chain (gamma-1 tubulin) (gamma-tubulin complex component 1) (gcp-1). [swissprot;acc:p23258]	0	3645.5	1.16907	3118.3
219	nif3-like protein 1 (amyotrophic lateral sclerosis 2 chromosomal region candidate gene protein 1) (my018 protein) (mds015). [swissprot;acc:q9gzt8]		8852.4	1.16896	7572.88
	transforming protein n-ras. [swissprot;acc:p01111]	1	16069.8	1.24711	12885.6
220	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [swissprot;acc:o60476]		41482.5	1.24361	33356.5
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	0	18704	1.16178	21730
221	cytohesin 1 (sec7 homolog b2-1). [swissprot;acc:q15438]	1	41482.5	1.24361	33356.5
	putative nucleoside diphosphate kinase (ec 2.7.4.6) (ndk) (ndp kinase). [swissprot;acc:o60361]	0	1905.84	1.15998	1643
222	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]		1499.4	1.15728	1735.23
	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [swissprot;acc:q99418]	1	41482.5	1.24361	33356.5
223	cytohesin 4. [swissprot;acc:q9uia0]
	hsp90 co-chaperone cdc37 (hsp90 chaperone protein kinase-targeting subunit) (p50cdc37). [swissprot;acc:q16543]	0	750.981	1.15407	650.724
224	60s ribosomal protein l7. [swissprot;acc:p18124]		1915.27	1.15183	2206.07
	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739]	1	41482.5	1.24361	33356.5
225	myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533]		9035	1.24114	7279.6
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	0	8763	1.15181	7608

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.