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 3708 to 3757 of 6456 in total

Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1

Rank	description	Network Comparison Type	red	green	network_comparison
1854	mln64 n-terminal domain homolog (stard3 n-terminal like protein). [swissprot;acc:o95772]	Subtracted	5458.12	5830.76	372.64
1855	keratin associated protein 4-2; keratin associated protein 4.2. [refseq;acc:nm_033062]	Divided	6076.66	6463.14	1.0636
	n-acetylglutamate synthase. [refseq;acc:nm_153006]	Subtracted	5162.27	5534.71	372.44
1856	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Divided	6076.66	6463.14	1.0636
	trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317]	Subtracted	4413.55	4784.6	371.05
1857	keratin associated protein 2-4; keratin associated protein 2.4. [refseq;acc:nm_033184]	Divided	6076.66	6463.15	1.0636
	transportin-sr; importin 12. [refseq;acc:nm_012470]	Subtracted	5184.94	5555.76	370.82
1858	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Divided	6076.66	6463.13	1.0636
	ruvb-like 1 (ec 3.6.1.-) (49-kda tata box-binding protein-interacting protein) (49 kda tbp-interacting protein) (tip49a) (pontin 52) (nuclear matrix protein 238) (nmp 238) (54 kda erythrocyte cytosolic protein) (ecp-54) (tip60-associated protein 54-alpha) (tap54-alpha). [swissprot;acc:q9y265]	Subtracted	5882.1	6252.66	370.56
1859	heat shock protein hsp 90-beta (hsp 84) (hsp 90). [swissprot;acc:p08238]		5733.71	6104.26	370.55
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Divided	6076.66	6463.13	1.0636
1860	40s ribosomal protein s24 (s19). [swissprot;acc:p16632]	Subtracted	5184.45	5554.97	370.52
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Divided	6076.66	6463.13	1.0636
1861	keratin associated protein 1.5. [refseq;acc:nm_031957]			6463.14
	splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427]	Subtracted	4331.35	4700.91	369.56
1862	26s proteasome non-atpase regulatory subunit 1 (26s proteasome regulatory subunit s1) (26s proteasome subunit p112). [swissprot;acc:q99460]		5826	6195.48	369.48
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Divided	6076.66	6463.13	1.0636
1863	adhesion regulating molecule 1 precursor (110 kda cell membrane glycoprotein) (gp110). [swissprot;acc:q16186]	Subtracted	5826	6195.48	369.48
	keratin, ultra high-sulfur matrix protein b (uhs keratin b) (uhs kerb). [swissprot;acc:o75690]	Divided	6076.66	6463.14	1.0636
1864	keratin, ultra high-sulfur matrix protein a (uhs keratin a) (uhs kera). [swissprot;acc:p26371]
	ubiquitin carboxyl-terminal hydrolase isozyme l5 (ec 3.4.19.12) (uch- l5) (ubiquitin thiolesterase l5) (ubiquitin c-terminal hydrolase uch37) (cgi-70) (ad-019). [swissprot;acc:q9y5k5]	Subtracted	5826	6195.48	369.48
1865	rna polymerase ii subunit 5-mediating protein (rpb5-mediating protein). [swissprot;acc:o94763]
	star-related lipid transfer protein 5 (stard5) (start domain- containing protein 5). [swissprot;acc:q9nsy2]	Divided	6076.66	6463.12	1.0636
1866	keratin associated protein 4.4. [refseq;acc:nm_032524]			6463.14
	translation initiation factor eif-2b epsilon subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q13144]	Subtracted	5369.43	5738.73	369.3
1867	alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7]	Divided	6076.66	6463.12	1.0636
	translation initiation factor eif-2b gamma subunit (eif-2b gdp-gtp exchange factor). [swissprot;acc:q9nr50]	Subtracted	5369.43	5738.73	369.3
1868	pinch protein (particularly interesting new cys-his protein) (lim and senescent cell antigen-like domains 1). [swissprot;acc:p48059]	Divided	6076.66	6463.12	1.0636
	rad17 homolog isoform 1; rad17-like protein; cell cycle checkpoint protein (rad17); rf-c activator 1 homolog. [refseq;acc:nm_002873]	Subtracted	5739.49	6108.72	369.23
1869	atp-dependent dna helicase ii, 70 kda subunit (lupus ku autoantigen protein p70) (ku70) (70 kda subunit of ku antigen) (thyroid-lupus autoantigen) (tlaa) (ctc box binding factor 75 kda subunit) (ctcbf) (ctc75). [swissprot;acc:p12956]
	integrin-linked protein kinase 1 (ec 2.7.1.-) (ilk-1) (59 kda serine/threonine protein kinase) (p59ilk). [swissprot;acc:q13418]	Divided	6076.66	6463.12	1.0636
1870	atp-dependent dna helicase ii, 80 kda subunit (lupus ku autoantigen protein p86) (ku86) (ku80) (86 kda subunit of ku antigen) (thyroid- lupus autoantigen) (tlaa) (ctc box binding factor 85 kda subunit) (ctcbf) (ctc85) (nuclear factor iv) (dna-repair protein xrcc5). [swissprot;acc:p13010]	Subtracted	5739.49	6108.72	369.23
	star-related lipid transfer protein 4 (stard4) (start domain- containing protein 4). [swissprot;acc:q96dr4]	Divided	6076.66	6463.13	1.0636
1871	nuclease sensitive element binding protein 1 (y box binding protein-1) (y-box transcription factor) (yb-1) (ccaat-binding transcription factor i subunit a) (cbf-a) (enhancer factor i subunit a) (efi-a) (dna-binding protein b) (dbpb). [swissprot;acc:p16991]	Subtracted	6682.05	7051.02	368.97
	ras suppressor protein 1 (rsu-1) (rsp-1). [swissprot;acc:q15404]	Divided	6076.66	6463.12	1.0636
1872	dna-binding protein a (cold shock domain protein a) (single-strand dna binding protein nf-gmb). [swissprot;acc:p16989]	Subtracted	6682.05	7051.02	368.97
	ras-gtpase-activating protein binding protein 1 (gap sh3-domain binding protein 1) (g3bp-1). [swissprot;acc:q13283]	Divided	6076.66	6463.12	1.0636
1873	40s ribosomal protein s11. [swissprot;acc:p04643]		3618.46	3402.09
	germ cell specific y-box binding protein; contrin. [refseq;acc:nm_015982]	Subtracted	6682.05	7051.02	368.97
1874	heat shock protein hsp 90-alpha (hsp 86). [swissprot;acc:p07900]		5746.06	6113.79	367.73
	ras-gtpase-activating protein binding protein 2 (gap sh3-domain binding protein 2) (g3bp-2). [swissprot;acc:q9un86]	Divided	6076.66	6463.12	1.0636
1875	atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031]	Subtracted	5106.13	5472.96	366.83
	keratin associated protein 1-3; keratin associated protein 1.3. [refseq;acc:nm_030966]	Divided	6076.66	6463.14	1.0636
1876	dna polymerase delta p38 subunit. [refseq;acc:nm_015584]	Subtracted	5106.13	5472.96	366.83
	espin. [refseq;acc:nm_031475]	Divided	6076.66	6463.12	1.0636
1877	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	Subtracted	5497.73	5132.35	365.38
	cytochrome p450 2d6 (ec 1.14.14.1) (cypiid6) (p450-db1) (debrisoquine 4-hydroxylase). [swissprot;acc:p10635]	Divided	6076.66	6463.12	1.0636
1878	dna-directed rna polymerases iii 12.5 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c11 subunit) (hsc11p) (hrpc11) (my010 protein). [swissprot;acc:q9y2y1]	Subtracted	5501.3	5866.02	364.72
	pleckstrin homology domain containing, family c (with ferm domain) member 1; mitogen inducible 2; kindlin 2. [refseq;acc:nm_006832]	Divided	6076.66	6463.12	1.0636
1879	lim and senescent cell antigen-like domains 2; ilk-binding protein. [refseq;acc:nm_017980]

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.