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

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Showing element 601 to 650 of 25824 in total

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

Rank	description	Value Type	red	green	network_comparison
151	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	Rooted	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
	septin 7 (cdc10 protein homolog). [swissprot;acc:q16181]	Squared	89182.8	125229	1.40418
159	necdin. [swissprot;acc:q99608]	Measured	23693.7	18263	1.29736
	regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6]	Ranked	249.663	298.263	1.19466
	rna-binding protein. [refseq;acc:nm_019027]	Rooted	52.7642	61.9019	1.17318
	septin 6. [swissprot;acc:q14141]	Squared	88953.6	124854	1.40359
160	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]	Rooted	52.7642	61.9019	1.17318
	guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471]	Ranked	249.663	298.263	1.19466
	homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017]	Squared	173408	242989	1.40126
	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	Measured	23693.7	18263	1.29736
161	homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483]	Squared	173408	242989	1.40126
	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	Measured	23693.7	18263	1.29736
	ns1-associated protein 1. [refseq;acc:nm_006372]	Rooted	52.7642	61.9019	1.17318
	rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	Ranked	249.663	298.263	1.19466
162	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]	Rooted	52.7642	61.9019	1.17318
	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Squared	173408	242989	1.40126
	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	Measured	23693.7	18263	1.29736
	nostrin. [refseq;acc:nm_052946]	Ranked	209.299	249.187	1.19058
163	eap30 subunit of ell complex. [refseq;acc:nm_007241]
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Rooted	52.7702	61.8915	1.17285

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.