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 2741 to 2790 of 3228 in total

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

Rank	description	red	green	network_comparison
2741	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]	198.278	198.321	1.00022
2742	nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494]
2743	nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289]
2744	transcriptional adaptor 3-like isoform a. [refseq;acc:nm_006354]	201.476	201.514	1.00019
2745	frg1 protein (fshd region gene 1 protein). [swissprot;acc:q14331]
2746	transcriptional adapter 2-like (ada2-like protein) (kl04p). [swissprot;acc:o75478]
2747	bromodomain containing 7; bromodomain protein; bromodomain-containing 7. [refseq;acc:nm_013263]	201.477		1.00018
2748	small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765]	189.563	189.531	1.00017
2749	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	190.522	190.496	1.00014
2750	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]
2751	proteasome subunit alpha type 1 (ec 3.4.25.1) (proteasome component c2) (macropain subunit c2) (multicatalytic endopeptidase complex subunit c2) (proteasome nu chain) (30 kda prosomal protein) (pros-30). [swissprot;acc:p25786]	215.338	215.312	1.00012
2752	p53-related protein kinase (ec 2.7.1.-) (nori-2). [swissprot;acc:q96s44]	221.7	221.716	1.00007
2753	serine--pyruvate aminotransferase (ec 2.6.1.51) (spt) (alanine-- glyoxylate aminotransferase) (ec 2.6.1.44) (agt). [swissprot;acc:p21549]	208.859	208.846	1.00006
2754	5-formyltetrahydrofolate cyclo-ligase (ec 6.3.3.2) (5,10-methenyl- tetrahydrofolate synthetase) (methenyl-thf synthetase) (mthfs). [swissprot;acc:p49914]	210.638	210.642	1.00002
2755	deoxyhypusine synthase (ec 2.5.1.46) (dhs). [swissprot;acc:p49366]	212.403	212.401	1.00001
2756	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	0.00001	0.00001	1
2757	nucleosome assembly protein 1-like 1 (nap-1 related protein). [swissprot;acc:p55209]
2758	nucleosome assembly protein 1-like 2 (brain-specific protein, x- linked). [swissprot;acc:q9ulw6]
2759	retinoic acid receptor rxr-alpha. [swissprot;acc:p19793]
2760	t-cell acute lymphocytic leukemia-2 protein (tal-2 protein). [swissprot;acc:q16559]
2761	guanine nucleotide-binding protein beta subunit-like protein 1 (g protein beta-subunit like protein 1) (wd40 repeat containing protein deleted in vcfs) (wdvcf protein) (fksg1 protein) (dgcrk3). [swissprot;acc:q9byb4]
2762	developmentally regulated gtp-binding protein 1 (drg 1). [swissprot;acc:q9y295]
2763	ring finger protein 3. [refseq;acc:nm_006315]
2764	ras-related protein rab-11b (gtp-binding protein ypt3). [swissprot;acc:q15907]
2765	histone h2a.e (h2a/e). [swissprot;acc:q99878]
2766	ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]
2767	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
2768	histone h2a.x (h2a/x). [swissprot;acc:p16104]
2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]
2770	nipsnap1 protein. [swissprot;acc:q9bpw8]
2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]
2772	uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]
2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
2774	dc12 protein. [refseq;acc:nm_020187]
2775	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]
2776	bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745]
2777	guanine nucleotide exchange factor mss4 (rab interacting factor). [swissprot;acc:p47224]
2778	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [sptrembl;acc:q8nhw3]
2779	caveolin-3 (m-caveolin). [swissprot;acc:p56539]
2780	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]
2781	exocyst complex component exo70. [swissprot;acc:q9upt5]
2782	vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [swissprot;acc:o75787]
2783	mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439]
2784	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]
2785	nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748]
2786	mab-21-like protein 1; mab-21-like 1. [refseq;acc:nm_005584]
2787	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]
2788	a-kinase anchor protein 5 (a-kinase anchor protein 79 kda) (akap 79) (camp-dependent protein kinase regulatory subunit ii high affinity binding protein) (h21). [swissprot;acc:p24588]
2789	protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [swissprot;acc:q06124]
2790	transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3]

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.