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 5530 to 5579 of 6456 in total

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

Rank	description	Network Comparison Type	red	green	network_comparison
2765	histone h2a.e (h2a/e). [swissprot;acc:q99878]	Subtracted	0	0	0
2766	ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2768	histone h2a.x (h2a/x). [swissprot;acc:p16104]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2769	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2770	nipsnap1 protein. [swissprot;acc:q9bpw8]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2771	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2772	uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2773	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2774	dc12 protein. [refseq;acc:nm_020187]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2775	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2776	bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2777	guanine nucleotide exchange factor mss4 (rab interacting factor). [swissprot;acc:p47224]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2778	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [sptrembl;acc:q8nhw3]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2779	caveolin-3 (m-caveolin). [swissprot;acc:p56539]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2780	importin alpha-2 subunit (karyopherin alpha-2 subunit) (srp1-alpha) (rag cohort protein 1). [swissprot;acc:p52292]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2781	exocyst complex component exo70. [swissprot;acc:q9upt5]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2782	vacuolar atp synthase membrane sector associated protein m8-9 (v-atpase m8.9 subunit). [swissprot;acc:o75787]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2783	mab-21-like protein 2; mab-21-like 2. [refseq;acc:nm_006439]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2784	histone h2a.a (h2a/a) (h2a.2). [swissprot;acc:p28001]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2785	nucleophosmin (npm) (nucleolar phosphoprotein b23) (numatrin) (nucleolar protein no38). [swissprot;acc:p06748]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2786	mab-21-like protein 1; mab-21-like 1. [refseq;acc:nm_005584]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2787	high mobility group protein 4-like (hmg-4l). [swissprot;acc:q9uj13]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
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]	Divided	0.00001	0.00001	1
		Subtracted	0	0	0
2790	transcription factor mafb (v-maf musculoaponeurotic fibrosarcoma oncogene homolog b). [swissprot;acc:q9y5q3]	Divided	0.00001	0.00001	1

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.