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

Results: HTML CSV LaTeX

Showing element 44 to 93 of 1892 in total

Network Comparison Type  : Subtracted
Interaction Map  : High confidence
Filtered  : 1
red  : 0
network_comparison  : 0
green  : 0

Rank	Hugo	Value Type	description
2766	SS18L1	Rooted	ss18-like protein 1 (syt homolog-1). [swissprot;acc:o75177]
2767	no value	Measured	histone h2a.c/d/i/n/p (h2a.1) (h2a/c) (h2a/d) (h2a/i) (h2a/n) (h2a/p) (h2a.1b). [swissprot;acc:p02261]
		Ranked
		Squared
		Rooted
2768	HIST2H2AB	Measured	histone h2a.x (h2a/x). [swissprot;acc:p16104]
		Ranked
		Squared
		Rooted
2769	HIST2H2AC	Measured	histone h2a.q (h2a/q) (h2a-gl101) (fragment). [swissprot;acc:q16777]
		Ranked
		Squared
		Rooted
2770	NIPSNAP1	Measured	nipsnap1 protein. [swissprot;acc:q9bpw8]
		Ranked
		Squared
		Rooted
2771	TBX1	Measured	t-box transcription factor tbx1 (t-box protein 1) (testis-specific t-box protein). [swissprot;acc:o43435]
		Ranked
		Squared
		Rooted
2772	NUDT14	Measured	uridine diphosphate glucose pyrophosphatase. [refseq;acc:nm_177533]
		Ranked
		Squared
		Rooted
2773	BMP8A	Measured	bone morphogenetic protein 8 precursor (bmp-8) (osteogenic protein 2) (op-2). [swissprot;acc:p34820]
		Ranked
		Squared
		Rooted
2774	C3orf37	Measured	dc12 protein. [refseq;acc:nm_020187]
		Ranked
		Squared
		Rooted
2775	JRKL	Measured	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]
		Ranked
		Squared
		Rooted
2776	BCOR	Measured	bcl-6 interacting corepressor isoform 1. [refseq;acc:nm_017745]
		Ranked
		Squared
		Rooted
2777	RABIF	Measured	guanine nucleotide exchange factor mss4 (rab interacting factor). [swissprot;acc:p47224]
		Ranked
		Squared
		Rooted
2778	MAFA	Measured	transcription factor mammalian mafa (pancreatic beta-cell specific transcriptional activator). [sptrembl;acc:q8nhw3]
		Ranked
		Squared
		Rooted
2779	CAV3	Measured	caveolin-3 (m-caveolin). [swissprot;acc:p56539]

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
- Hugo is the HGNC identifier if it exists
- 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.