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

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Showing element 168 to 217 of 3228 in total

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

Rank	description	network_comparison	red	green
168	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	1.29736	23693.7	18263
169	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]
170	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]
171	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]
172	trophinin. [swissprot;acc:q12816]
173	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	1.29727	4579.34	5940.64
174	mad protein (max dimerizer). [swissprot;acc:q05195]	1.2958	4455.95	5774.03
175	max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539]	1.29553	4456.67	5773.77
176	max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582]	1.29544	4456.93	5773.67
177	max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300]	1.29539	4457.06	5773.63
178	myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0]	1.29238	21591.5	27904.5
179	myosin vc (myosin 5c). [swissprot;acc:q9nqx4]
180	myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1]
181	eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760]	1.29102	4068.56	5252.6
182	rna-binding protein. [refseq;acc:nm_019027]	1.29051	4069.83	5252.17
183	apobec-1 complementation factor isoform 1; apobec-1 stimulating protein; apo-b rna editing protein. [refseq;acc:nm_014576]
184	ns1-associated protein 1. [refseq;acc:nm_006372]
185	heterogeneous nuclear ribonucleoprotein r (hnrnp r). [swissprot;acc:o43390]
186	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	1.29001	4071.1	5251.75
187	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	1.28807	4569.48	5885.79
188	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	1.28281	4571.89	5864.86
189	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]
190	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]
191	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	1.27712	4638.1	5923.4
192	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	1.26767	17757.5	14008
193	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	1.26766	17756.5	14007.3
194	cyclin g2. [swissprot;acc:q16589]	1.26743	17738.6	13995.7
195	cyclin g1 (cyclin g). [swissprot;acc:p51959]		17738.5	13995.6
196	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	1.26742		13995.7
197	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]
198	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	1.26708	17710.9	13977.7
199	serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323]	1.26455	4916.8	3888.18
200	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	1.26315	4808.79	6074.21
201	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	1.26294	4810.22	6075.04
202	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]	1.26269	4812.01	6076.09
203	autophagy protein 12-like (apg12-like). [swissprot;acc:o94817]	1.25723	11757.8	9352.11
204	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	1.25339	4512.19	5655.52
205	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]
206	atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915]	1.24965	5720.25	4577.5
207	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	1.24946	4771.21	5961.43
208	voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5]	1.24907	4068.78	5082.18
209	voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]
210	voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698]	1.24906	4068.82	5082.21
211	voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1]	1.24905	4068.91	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]	1.24896	4446.72	5553.79
213	nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983]
214	voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02]	1.24827	4074.83	5086.49
215	transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116]	1.24717	16074	12888.4
216	leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13]	1.24714	16071.6	12886.8
217	ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]

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.