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

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Showing element 1630 to 1679 of 12912 in total

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

Rank	Value Type	description	red	green	network_comparison
408	Ranked	ccaat-box-binding transcription factor (ccaat-binding factor) (cbf). [swissprot;acc:q03701]	255.112	234.804	1.08649
	Squared	probable serine protease htra3 precursor (ec 3.4.21.-). [swissprot;acc:p83110]	18995.7	23244.7	1.22368
	Rooted	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]	49.9856	45.4432	1.09996
409	Measured	docking protein 2 (p56(dok-2)) (downstream of tyrosine kinase 2). [swissprot;acc:o60496]	6102.59	7081.46	1.1604
	Ranked	rna polymerase i associated factor 53. [refseq;acc:nm_022490]	241.045	261.874	1.08641
	Squared	serine protease htra1 precursor (ec 3.4.21.-) (l56). [swissprot;acc:q92743]	18995.6	23242.8	1.22359
	Rooted	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	50.4409	45.8795	1.09942
410	Measured	docking protein 1 (p62(dok)) (downstream of tyrosine kinase 1) (pp62). [swissprot;acc:q99704]	6102.59	7081.46	1.1604
	Ranked	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	233.376	253.539	1.0864
	Squared	crk-associated substrate (p130cas) (breast cancer anti-estrogen resistance 1 protein). [swissprot;acc:p56945]	19546.1	23881.6	1.22181
	Rooted	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	55.5489	50.535	1.09922
411	Measured	tyrosine-protein kinase frk (ec 2.7.1.112) (nuclear tyrosine protein kinase rak). [swissprot;acc:p42685]	6102.59	7081.46	1.1604
	Ranked	tfiih basal transcription factor complex p62 subunit (basic transcription factor 62 kda subunit) (btf2-p62) (general transcription factor iih polypeptide 1). [swissprot;acc:p32780]	233.376	253.539	1.0864
	Squared	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	17861.2	21821.8	1.22174
	Rooted	pp3111 protein. [refseq;acc:nm_022156]	55.5489	50.535	1.09922
412	Measured	mki67 (fha domain) interacting nucleolar phosphoprotein; nucleolar phosphoprotein nopp34; nucleolar protein interacting with the fha domain of pki-67. [refseq;acc:nm_032390]	3594.31	4169.95	1.16015
	Ranked	ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (ec 1.10.2.2) (rieske iron-sulfur protein) (risp). [swissprot;acc:p47985]	240.788	261.416	1.08567
	Squared	t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991]	19556	23891.8	1.22171
	Rooted	syntaxin 18. [swissprot;acc:q9p2w9]	55.5489	50.535	1.09922
413	Measured	vav proto-oncogene. [swissprot;acc:p15498]	6644.99	7707.8	1.15994
	Ranked	dna-directed rna polymerase i 40 kda polypeptide (ec 2.7.7.6) (rpa40) (rpa39). [swissprot;acc:o15160]	240.913	261.45	1.08525
	Squared	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]	19568.3	23904.6	1.2216
	Rooted	rd protein. [swissprot;acc:p18615]	55.5489	50.535	1.09922
414	Measured	autophagy protein 5-like (apg5-like) (apoptosis-specific protein). [swissprot;acc:q9h1y0]	6744.05	5815.13	1.15974
	Ranked	katanin p60 subunit a 1. [refseq;acc:nm_007044]	232.431	252.238	1.08522
	Squared	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	22109.6	26989.4	1.22071
	Rooted	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	55.5489	50.535	1.09922
415	Measured	vav-3 protein. [swissprot;acc:q9ukw4]	6647.43	7706.18	1.15927
	Ranked	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	232.382	252.166	1.08514
	Squared	vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504]	29160.4	35570.2	1.21981
	Rooted	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	55.5489	50.535	1.09922
416	Measured	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	4509.54	5223.95	1.15842
	Ranked	dna-directed rna polymerase i 135 kda polypeptide (ec 2.7.7.6) (rna polymerase i subunit 2) (rpa135). [swissprot;acc:q9h9y6]	240.6	261.041	1.08496
	Squared	prohibitin. [swissprot;acc:p35232]	22841.8	27856.2	1.21953
	Rooted	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	55.5489	50.535	1.09922
417	Measured	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	4522.71	5233.14	1.15708
	Ranked	set domain and mariner transposase fusion gene. [refseq;acc:nm_006515]	233.539	253.197	1.08417
	Squared	repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]	22841.8	27856.2	1.21953
	Rooted	j domain containing protein 1. [swissprot;acc:q9ukb3]	55.5489	50.535	1.09922
418	Measured	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [refseq;acc:nm_005872]	5493.1	6350.19	1.15603
	Ranked	cd209 antigen-like; putative type ii membrane protein. [refseq;acc:nm_014257]	233.539	253.197	1.08417
	Squared	e-1 enzyme. [refseq;acc:nm_021204]	30903.8	37638.1	1.21791
	Rooted	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	55.5489	50.535	1.09922
419	Measured	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [refseq;acc:nm_001253]	5493.1	6350.19	1.15603
	Ranked	low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734]	233.539	253.197	1.08417
	Squared	apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772]	24832.1	30242.8	1.21789
	Rooted	ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]	55.5489	50.535	1.09922
420	Measured	hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492]	10235.2	11830.8	1.15589
	Ranked	cd209 antigen; dendritic cell-specific icam3-grabbing nonintegrin. [refseq;acc:nm_021155]	233.539	253.197	1.08417
	Squared	60s ribosomal protein l24 (l30). [swissprot;acc:p38663]	30924.3	37652.3	1.21756

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.