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

Results: HTML CSV LaTeX

Showing element 5208 to 5257 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2604	lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893]	Divided	7572.7	7689.04	1.01536
2605	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [swissprot;acc:q9nqt5]	Subtracted	4921.84	5005.06	83.22
	lim/homeobox protein lhx4. [swissprot;acc:q969g2]	Divided	7573.83	7689.81	1.01531
2606	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [swissprot;acc:q9nqt4]	Subtracted	4921.84	5005.06	83.22
	tyrosyl-trna synthetase (ec 6.1.1.1) (tyrosyl--trna ligase) (tyrrs). [swissprot;acc:p54577]	Divided	4450.84	4517.54	1.01499
2607	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4]	Subtracted	5599.85	5683	83.15
	stromal interaction molecule 1 precursor. [swissprot;acc:q13586]	Divided	6380.61	6476.19	1.01498
2608	cab2. [refseq;acc:nm_033419]	Subtracted	5599.85	5683	83.15
	trap/mediator complex component trap25. [refseq;acc:nm_080651]	Divided	6380.6	6476.18	1.01498
2609	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]	Subtracted	5599.85	5683	83.15
	wd repeat- and fyve domain-containing protein 2; wd40 and fyve domain containing 2. [refseq;acc:nm_052950]	Divided	6380.84	6476.41	1.01498
2610	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685]	Subtracted	5599.85	5683	83.15
	serine/threonine-protein kinase pak 4 (ec 2.7.1.-) (p21-activated kinase 4) (pak-4). [swissprot;acc:o96013]	Divided	6380.61	6476.19	1.01498
2611	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]	Subtracted	5599.85	5683	83.15
	polyposis locus protein 1 (tb2 protein). [swissprot;acc:q00765]	Divided	6380.6	6476.18	1.01498
2612	acyl-coa dehydrogenase, medium-chain specific, mitochondrial precursor (ec 1.3.99.3) (mcad). [swissprot;acc:p11310]		6380.61	6476.19
	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]	Subtracted	5599.85	5683	83.15
2613	histone h4. [swissprot;acc:p02304]		6072.17	6155.08	82.91
	polyposis locus protein 1-like 1; likely ortholog of mouse polyposis locus protein 1-like 1. [refseq;acc:nm_138393]	Divided	6380.6	6476.18	1.01498
2614	protein kinase nyd-sp25. [refseq;acc:nm_033516]	Subtracted	6527.56	6608.61	81.05
	stromal interaction molecule 2 precursor. [swissprot;acc:q9p246]	Divided	6380.61	6476.19	1.01498
2615	katanin p60 subunit a 1. [refseq;acc:nm_007044]	Subtracted	4327.94	4248.77	79.17
	serine/threonine-protein kinase pak 7 (ec 2.7.1.-) (p21-activated kinase 7) (pak-7) (pak-5). [swissprot;acc:q9p286]	Divided	6380.61	6476.19	1.01498
2616	katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886]	Subtracted	4331.39	4252.8	78.59
	wd repeat and fyve domain containing 1 isoform 1; phosphoinositide-binding protein sr1; wd40 and fyve domain containing 1. [refseq;acc:nm_020830]	Divided	6380.32	6475.92	1.01498
2617	dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4]		5599.85	5683	1.01485
	t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711]	Subtracted	3964.71	4042.75	78.04
2618	cab2. [refseq;acc:nm_033419]	Divided	5599.85	5683	1.01485
	homeobox protein barh-like 1. [swissprot;acc:q9hbu1]	Subtracted	3964.71	4042.75	78.04
2619	dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953]	Divided	5599.85	5683	1.01485
	opsin 4 (melanopsin). [swissprot;acc:q9uhm6]	Subtracted	3964.71	4042.75	78.04
2620	dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685]	Divided	5599.85	5683	1.01485
	t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]	Subtracted	3964.71	4042.75	78.04
2621	eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055]	Divided	5599.85	5683	1.01485
	t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]	Subtracted	3964.71	4042.75	78.04
2622	hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
	suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553]	Divided	5599.85	5683	1.01485
2623	adapter-related protein complex 3 beta 1 subunit (beta-adaptin 3a) (ap-3 complex beta-3a subunit) (beta-3a-adaptin). [swissprot;acc:o00203]		6815.24	6916.14	1.01481
	homeobox protein barh-like 2. [swissprot;acc:q9umq3]	Subtracted	3964.71	4042.75	78.04
2624	ny-ren-24 antigen (fragment). [sptrembl;acc:q9y5a4]	Divided	6815.24	6916.14	1.01481
	ras-related protein rab-37. [swissprot;acc:q96ax2]	Subtracted	3852.99	3775.86	77.13
2625	adapter-related protein complex 3 beta 2 subunit (beta-adaptin 3b) (ap-3 complex beta-3b subunit) (beta-3b-adaptin) (neuron-specific vesicle coat protein beta-nap). [swissprot;acc:q13367]	Divided	6815.24	6916.14	1.01481
	ras-related protein rab-26. [swissprot;acc:q9ulw5]	Subtracted	3852.99	3775.86	77.13
2626	dna-directed rna polymerase ii 33 kda polypeptide (ec 2.7.7.6) (rpb3) (rna polymerase ii subunit 3) (rpb33) (rpb31). [swissprot;acc:p19387]
	insulin gene enhancer protein isl-1 (islet-1). [swissprot;acc:p20663]	Divided	7424.26	7534.05	1.01479
2627	3-phosphoinositide dependent protein kinase-1 (ec 2.7.1.37) (hpdk1). [swissprot;acc:o15530]	Subtracted	3370.46	3444.18	73.72
	ubiquitin-specific protease otubain 1. [refseq;acc:nm_017670]	Divided	7135.64	7240.5	1.0147
2628	40s ribosomal protein s9. [swissprot;acc:p46781]		3933.74	3877.14	1.0146
	deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398]	Subtracted	4180.32	4253.46	73.14
2629	dna-directed rna polymerase ii 14.4 kda polypeptide (ec 2.7.7.6) (rpb6) (rpb14.4) (rpabc2). [swissprot;acc:p41584]	Divided	4582.38	4649.17	1.01458

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.