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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.

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

Results: HTML CSV LaTeX

Showing element 25776 to 25825 of 29840 in total

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

Rank	description	red	green	Network Comparison Type	network_comparison
1196	scy1-like 1; telomerase regulation-associated protein; ht019 protein; telomerase regulation-associated protein; n-terminal kinase-like protein; teratoma-associated tyrosine kinase; n-terminal kinase-like. [refseq;acc:nm_020680]	59.9298	62.8125	Subtracted	2.8827
1197	heat shock factor binding protein 1. [swissprot;acc:o75506]	62.6382	65.5533	Divided	1.04654
	nuclear pore complex protein nup98 (nucleoporin nup98) (98 kda nucleoporin). [swissprot;acc:p52948]	59.9298	62.8125	Subtracted	2.8827
1198	ammecr1 protein. [refseq;acc:nm_015365]
	homeobox protein otx2. [swissprot;acc:p32243]	56.0239	58.6274	Divided	1.04647
1199	mrna-associated protein mrnp 41 (rae1 protein homolog). [swissprot;acc:p78406]	59.9298	62.8125	Subtracted	2.8827
	pxr2b protein. [refseq;acc:nm_016559]	66.7327	69.832	Divided	1.04644
1200	homeobox protein otx1. [swissprot;acc:p32242]	56.0736	58.677		1.04643
	zinc finger protein zic 3 (zinc finger protein of the cerebellum 3). [swissprot;acc:o60481]	61.4869	64.3691	Subtracted	2.8822
1201	cone-rod homeobox protein. [swissprot;acc:o43186]	56.0896	58.6931	Divided	1.04642
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	68.9332	71.8139	Subtracted	2.8807
1202	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]
	myb-related protein b (b-myb). [swissprot;acc:p10244]	60.1108	62.9002	Divided	1.0464
1203	myb-related protein a (a-myb). [swissprot;acc:p10243]	60.1161	62.9033		1.04636
	transducin beta-like 1x protein (transducin-beta-like 1, x-linked). [swissprot;acc:o60907]	68.9332	71.8139	Subtracted	2.8807
1204	protein ad-016 (protein cgi-116) (x0009). [swissprot;acc:q9y3c0]	63.2865	66.2117	Divided	1.04622
	transducin beta-like 1y protein (transducin-beta-like 1, y-linked). [swissprot;acc:q9bq87]	68.9332	71.8139	Subtracted	2.8807
1205	protein kinase clk2 (ec 2.7.1.-) (cdc-like kinase 2). [swissprot;acc:p49760]	64.7548	67.7419	Divided	1.04613
	zinc finger protein zic 2 (zinc finger protein of the cerebellum 2). [swissprot;acc:o95409]	61.4866	64.3673	Subtracted	2.8807
1206	similar to lim domain only 7 (fragment). [sptrembl;acc:q8n6m2]	62.5668	65.4521	Divided	1.04612
	u3 small nucleolar ribonucleoprotein protein mpp10 (m phase phosphoprotein 10). [swissprot;acc:o00566]	52.2349	55.1039	Subtracted	2.869
1207	camp response element-binding protein cre-bpa. [refseq;acc:nm_004904]	61.4842	64.3512		2.867
	p10-binding protein. [refseq;acc:nm_024491]	60.7029	63.5018	Divided	1.04611
1208	protein kinase clk3 (ec 2.7.1.-) (cdc-like kinase 3). [swissprot;acc:p49761]	64.7526	67.7372		1.04609
	scratch; scratch 1. [refseq;acc:nm_031309]	67.9472	70.8115	Subtracted	2.8643
1209	fibulin-2 precursor. [swissprot;acc:p98095]	76.496	79.3591		2.8631
	homeobox protein six1 (sine oculis homeobox homolog 1). [swissprot;acc:q15475]	61.3914	64.2183	Divided	1.04605
1210	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	67.9155	70.7734	Subtracted	2.8579
	proliferation-associated protein 2g4 (cell cycle protein p38-2g4 homolog) (hg4-1). [swissprot;acc:q9uq80]	61.3876	64.2125	Divided	1.04602
1211	dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388]	67.2521	70.3462		1.04601
	ornithine decarboxylase (ec 4.1.1.17) (odc). [swissprot;acc:p11926]	67.3577	70.2116	Subtracted	2.8539
1212	aminoadipate-semialdehyde synthase; lysine-ketoglutarate reductase /saccharopine dehydrogenase; lysine-2-oxoglutarate reductase; aminoadipic semialdehyde synthase. [refseq;acc:nm_005763]	67.3443	70.1972		2.8529
	homeobox protein six2 (sine oculis homeobox homolog 2). [swissprot;acc:q9npc8]	61.3832	64.2055	Divided	1.04598
1213	40s ribosomal protein s8. [swissprot;acc:p09058]	61.4774	64.3044
	ornithine decarboxylase-like protein (ec 4.1.1.17) (odc-paralogue) (odc-p). [swissprot;acc:q96a70]	67.3368	70.189	Subtracted	2.8522
1214	dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880]	67.2519	70.3434	Divided	1.04597
	ornithine decarboxylase antizyme inhibitor. [swissprot;acc:o14977]	67.3352	70.1873	Subtracted	2.8521
1215	mitotic checkpoint protein bub3. [swissprot;acc:o43684]	60.2183	62.9735	Divided	1.04575
	rab3a interacting protein (rabin3)-like 1. [refseq;acc:nm_013401]	65.6777	68.5272	Subtracted	2.8495
1216	trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646]	66.2263	69.0756		2.8493
	zinc finger protein 207. [swissprot;acc:o43670]	60.2183	62.9735	Divided	1.04575
1217	cyclic-amp-dependent transcription factor atf-7 (activating transcription factor 7) (transcription factor atf-a). [swissprot;acc:p17544]	61.4717	64.2826		1.04573
	trimethyllysine dioxygenase, mitochondrial precursor (ec 1.14.11.8) (epsilon-trimethyllysine 2-oxoglutarate dioxygenase) (tml-alpha- ketoglutarate dioxygenase) (tml hydroxylase) (tml dioxygenase) (tmld). [swissprot;acc:q9nvh6]	64.9605	67.8088	Subtracted	2.8483
1218	gtp-binding protein era homolog (hera) (fragment). [swissprot;acc:o75616]
	hiv-1 rev binding protein 2; rev interacting protein. [refseq;acc:nm_007043]	51.9837	54.3601	Divided	1.04571
1219	cyclic-amp-dependent transcription factor atf-2 (activating transcription factor 2) (camp response element binding protein cre- bp1) (hb16). [swissprot;acc:p15336]	61.4767	64.2857		1.04569
	rab3a interacting protein isoform alpha 1; rabin3; ssx2 interacting protein. [refseq;acc:nm_022456]	65.6542	68.5013	Subtracted	2.8471
1220	dead-box protein 4 (vasa homolog). [swissprot;acc:q9nqi0]	58.0178	60.6658	Divided	1.04564
	nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3]	53.4366	56.2771	Subtracted	2.8405
1221	glycerol-3-phosphate transporter (g-3-p transporter) (g-3-p permease). [swissprot;acc:p57057]	66.3775	69.4004	Divided	1.04554

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.