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

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Showing element 582 to 631 of 12912 in total

Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Value Type	red	green	network_comparison
146	huntingtin interacting protein c. [refseq;acc:nm_012272]	Rooted	55.0737	66.0298	1.19894
	kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193]	Ranked	265.632	319.531	1.20291
	ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	Squared	103496	146848	1.41888
147	forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457]	Rooted	42.0574	50.4237	1.19893
	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Ranked	50.7983	42.3003	1.2009
	putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453]	Measured	11068	8508.5	1.30082
	ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	Squared	103496	146848	1.41888
148	associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463]	Measured	11068	8508.5	1.30082
	forkhead box protein p1 (hspc215). [swissprot;acc:q9h334]	Rooted	42.0577	50.424	1.19892
	ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	Squared	103496	146848	1.41888
	sad1/unc-84 protein-like 1. [swissprot;acc:o94901]	Ranked	296.677	247.559	1.19841
149	anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685]	Squared	103496	146848	1.41888
	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	Ranked	142	170	1.19718
	forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1]	Rooted	42.0684	50.4323	1.19882
	neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079]	Measured	11068	8508.5	1.30082
150	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	Ranked	55	46	1.19565
	pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989]	Squared	121200	85473.4	1.41799
	protein hspc134 (protein cda04). [swissprot;acc:q9by43]	Measured	11068	8508.5	1.30082
	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	Rooted	63.5827	53.0856	1.19774
151	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]		38.8223	46.4975	1.1977
	deoxyribonuclease ii beta isoform 1 precursor; deoxyribonuclease ii beta; endonuclease dlad. [refseq;acc:nm_021233]	Squared	250303	354894	1.41786
	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]	Ranked	55	46	1.19565
	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]	Measured	4578.09	5939.91	1.29746
152	luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019]	Rooted	55.2859	65.9288	1.19251
	melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801]	Measured	23693.7	18263	1.29736
	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]	Ranked	55	46	1.19565
	septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599]	Squared	90226	126939	1.4069
153	chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286]	Ranked	249.663	298.263	1.19466
	hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703]	Measured	23693.7	18263	1.29736
	luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032]	Rooted	55.297	65.9236	1.19217
	ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858]	Squared	70011	49783	1.40632
154	eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010]	Rooted	43.5479	51.5473	1.18369
	melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357]	Measured	23693.7	18263	1.29736
	regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795]	Ranked	249.663	298.263	1.19466
	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	Squared	42788.3	60162.6	1.40605
155	cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240]		126408	89940.5	1.40546
	melanoma-associated antigen 11 (mage-11 antigen). [swissprot;acc:p43364]	Measured	23693.7	18263	1.29736
	putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37]	Ranked	249.663	298.263	1.19466
	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330]	Rooted	55.7423	65.6839	1.17835
156	melanoma-associated antigen 2 (mage-2 antigen). [swissprot;acc:p43356]	Measured	23693.7	18263	1.29736
	regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081]	Ranked	249.663	298.263	1.19466
	septin 10 isoform 1. [refseq;acc:nm_144710]	Squared	89578.7	125883	1.40528
	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]	Rooted	56.3447	66.124	1.17356
157	brain protein 44. [swissprot;acc:o95563]	Squared	89182.8	125229	1.40418
	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	Rooted	52.7582	61.9123	1.17351
	hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932]	Measured	23693.7	18263	1.29736
	transcription factor lbx1. [swissprot;acc:p52954]	Ranked	249.663	298.263	1.19466
158	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	Rooted	56.3507	66.1252	1.17346
	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360]	Measured	23693.7	18263	1.29736
	mosaic protein lgn. [swissprot;acc:p81274]	Ranked	249.663	298.263	1.19466

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.