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

Results: HTML CSV LaTeX

Showing element 312 to 361 of 1892 in total

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

Rank	Hugo	description	Value Type
2833	TPM4	tropomyosin alpha 4 chain (tropomyosin 4) (tm30p1). [swissprot;acc:p07226]	Rooted
2834	ATP5L	atp synthase g chain, mitochondrial (ec 3.6.3.14) (atpase subunit g). [swissprot;acc:o75964]	Measured
			Ranked
			Squared
			Rooted
2835	UGT1A9	udp-glucuronosyltransferase 1-6 precursor, microsomal (ec 2.4.1.17) (udp-glucuronosyltransferase 1a6) (udpgt) (ugt1*6) (ugt1-06) (ugt1.6) (ugt-1f) (ugt1f) (phenol-metabolizing udp-glucuronosyltransferase). [swissprot;acc:p19224]	Measured
			Ranked
			Squared
			Rooted
2836	COG1	conserved oligomeric golgi complex component 1. [swissprot;acc:q8wtw3]	Measured
			Ranked
			Squared
			Rooted
2837	TK2	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]	Measured
			Ranked
			Squared
			Rooted
2838	DCHS1	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Measured
			Ranked
			Squared
			Rooted
2839	TAF10	transcription initiation factor tfiid 30 kda subunit (tafii-30) (tafii30). [swissprot;acc:q12962]	Measured
			Ranked
			Squared
			Rooted
2840	CUL5	vasopressin-activated calcium-mobilizing receptor (vacm-1) (cullin homolog 5) (cul-5). [swissprot;acc:q93034]	Measured
			Ranked
			Squared
			Rooted
2841	COPS2	cop9 signalosome complex subunit 2 (signalosome subunit 2) (sgn2) (thyroid receptor interacting protein 15) (trip15). [swissprot;acc:q15647]	Measured
			Ranked
			Squared
			Rooted
2842	NOLC1	nucleolar phosphoprotein p130 (nucleolar 130 kda protein) (140 kda nucleolar phosphoprotein) (nopp140) (nucleolar and coiled-body phosphoprotein 1). [swissprot;acc:q14978]	Measured
			Ranked
			Squared
			Rooted
2843	SENP8	sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8]	Measured
			Ranked
			Squared
			Rooted
2844	FBN1	fibrillin 1 precursor. [swissprot;acc:p35555]	Measured
			Ranked
			Squared
			Rooted
2845	PACSIN3	protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [swissprot;acc:q9uks6]	Measured
			Ranked
			Squared
			Rooted
2846	C10orf118	ctcl tumor antigen l14-2. [refseq;acc:nm_018017]	Measured

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.