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

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Showing element 2280 to 2329 of 3228 in total

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

description	Rank	red	green	network_comparison
pyruvate dehydrogenase e1 component beta subunit, mitochondrial precursor (ec 1.2.4.1) (pdhe1-b). [swissprot;acc:p11177]	2450	6737.15	6957.34	1.03268
pyruvate kinase, m1 isozyme (ec 2.7.1.40) (pyruvate kinase muscle isozyme) (cytosolic thyroid hormone-binding protein) (cthbp) (thbp1). [swissprot;acc:p14618]	1806	4783.49	5097.66	1.06568
quaking isoform 6. [sptrembl;acc:q9p0x9]	2224	5864.49	6145.14	1.04786
r3h domain (binds single-stranded nucleic acids) containing-like. [refseq;acc:nm_178491]	3132	0.00001	0.00001	1
r3h domain protein 1. [swissprot;acc:q15032]	2080	5837.34	6162.91	1.05577
rab acceptor 1 (prenylated); prenylated rab acceptor 1. [refseq;acc:nm_006423]	1137	5790.65	6303.92	1.08864
rab coupling protein; rab-interacting recycling protein; rab effector protein; rab11-family interacting protein 1. [refseq;acc:nm_025151]	1449	5602.01	6031.05	1.07659
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	3119	0.00001	0.00001	1
rab gdp dissociation inhibitor beta (rab gdi beta) (gdi-2). [swissprot;acc:p50395]	3193
rab geranylgeranyltransferase alpha subunit (ec 2.5.1.-) (rab geranyl- geranyltransferase alpha subunit) (rab gg transferase alpha) (rab ggtase alpha). [swissprot;acc:q92696]	3134
rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401]	1109	6545.19	7132.89	1.08979
rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456]	1111	6540.61	7127.41	1.08972
rabaptin, rab gtpase binding effector protein 1; rabaptin-5; neurocrescin. [refseq;acc:nm_004703]	1737	5925.65	6326.43	1.06763
rac gtpase activating protein 1; gtpase activating protein. [refseq;acc:nm_013277]	1941	5521.07	5856.93	1.06083
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749]	542	3889.27	4426.74	1.13819
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751]	545
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243]	544
rad1 homolog isoform 1; exonuclease homolog rad1; cell cycle checkpoint protein rad1 a/b; rad1-like protein; cell cycle checkpoint protein hrad1; dna repair exonuclease (rec1); dna repair protein rad1; rad1-like dna damage checkpoint protein. [refseq;acc:nm_002853]	2111	6916.14	7295.24	1.05481
rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	1837	5739.49	6108.72	1.06433
rad50 homolog isoform 1. [refseq;acc:nm_005732]	2601	7222.12	7110.74	1.01566
rad50-interacting protein 1. [refseq;acc:nm_021930]	1	450.5	2394.5	5.31521
rad54-like protein; rad54 homolog. [refseq;acc:nm_003579]	1260	5754.84	6232.83	1.08306
rad9 homolog; cell cycle checkpoint control protein; rad9 homolog (s. pombe). [refseq;acc:nm_004584]	2027	6218.34	6575.81	1.05749
raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	193	17756.5	14007.3	1.26766
ral guanine nucleotide dissociation stimulator (ralgef) (ralgds). [swissprot;acc:q12967]	267	14021.4	11523	1.21682
ral guanine nucleotide dissociation stimulator-like 1 (ralgds-like 1). [swissprot;acc:q9nzl6]	295	13261.9	11017.8	1.20368
ral guanine nucleotide dissociation stimulator-like 2 (ralgds-like factor) (ras-associated protein rab2l). [swissprot;acc:o15211]	217	16071.6	12886.8	1.24714
ral guanine nucleotide exchange factor ralgps1a. [refseq;acc:nm_014636]	2347	6480.27	6765.81	1.04406
ral-a exchange factor ralgps2. [refseq;acc:nm_152663]	2348
rala binding protein 1; rala-binding protein. [refseq;acc:nm_006788]	3212	0.00001	0.00001	1
ran binding protein 11. [refseq;acc:nm_016338]	1032	6138.91	6717.05	1.09418
ran binding protein 3 isoform ranbp3-d; ran-binding protein-3. [refseq;acc:nm_007322]	3202	0.00001	0.00001	1
ran-binding protein 2 (ranbp2) (nuclear pore complex protein nup358) (nucleoporin nup358) (358 kda nucleoporin) (p270). [swissprot;acc:p49792]	2082	5800.93	6123.38	1.05559
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260]	2083	5799.84	6122.18	1.05558
	2084	5800.22	6122.6
ran-gtp binding protein (fragment). [sptrembl;acc:o60518]	906	6165.1	6783.01	1.10023
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736]	282	3119.98	2579.49	1.20953
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2]	14	398.5	1281.5	3.21581
ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]	1871	6076.66	6463.12	1.0636
ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]	1872
ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]	1874
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154]	1997	5047.2	5344.68	1.05894
ras-related c3 botulinum toxin substrate 2 (p21-rac2) (small g protein) (gx). [swissprot;acc:p15153]	2000
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658]	1998
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570]	319	20911	24908.5	1.19117
ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064]	321
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157]	320
ras-related protein rab-11a (rab-11) (24kg) (yl8). [swissprot;acc:p24410]	3112	0.00001	0.00001	1
ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]	2764
ras-related protein rab-1a (ypt1-related protein). [swissprot;acc:p11476]	2961

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.