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

Results: HTML CSV LaTeX

Showing element 962 to 1011 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
2996	RBM8A	rna-binding protein 8a (rna binding motif protein 8a) (ribonucleoprotein rbm8a) (rna-binding protein y14) (binder of ovca1- 1) (bov-1). [swissprot;acc:q9y5s9]	Ranked
			Squared
			Rooted
2997	PSME3	proteasome activator complex subunit 3 (proteasome activator 28-gamma subunit) (pa28gamma) (pa28g) (activator of multicatalytic protease subunit 3) (11s regulator complex gamma subunit) (reg-gamma) (ki nuclear autoantigen). [swissprot;acc:q12920]	Measured
			Ranked
			Squared
			Rooted
2998	ZFYVE20	fyve-finger-containing rab5 effector protein rabenosyn-5. [refseq;acc:nm_022340]	Measured
			Ranked
			Squared
			Rooted
2999	TAF4	transcription initiation factor tfiid 135 kda subunit (tafii-135) (tafii135) (tafii-130) (tafii130). [swissprot;acc:o00268]	Measured
			Ranked
			Squared
			Rooted
3000	PXDN	myeloblast kiaa0230 (fragment). [sptrembl;acc:q92626]	Measured
			Ranked
			Squared
			Rooted
3001	NEDD8	ubiquitin-like protein nedd8. [swissprot;acc:q15843]	Measured
			Ranked
			Squared
			Rooted
3002	CCNT1	cyclin t1 (cyclin t) (cyct1). [swissprot;acc:o60563]	Measured
			Ranked
			Squared
			Rooted
3003	LRRC6	testis specific leucine rich repeat protein. [refseq;acc:nm_012472]	Measured
			Ranked
			Squared
			Rooted
3004	SNRPN	small nuclear ribonucleoprotein associated protein n (snrnp-n) (sm protein n) (sm-n) (smn) (sm-d) (tissue-specific splicing protein). [swissprot;acc:p14648]	Measured
			Ranked
			Squared
			Rooted
3005	NDUFA5	nadh-ubiquinone oxidoreductase 13 kda-b subunit (ec 1.6.5.3) (ec 1.6.99.3) (complex i-13kd-b) (ci-13kd-b) (complex i subunit b13). [swissprot;acc:q16718]	Measured
			Ranked
			Squared
			Rooted
3006	DGCR8	dgcr8 protein (digeorge syndrome critical region 8). [swissprot;acc:q8wyq5]	Measured
			Ranked
			Squared
			Rooted
3007	YEATS4	glioma-amplified sequence-41; numa binding protein 1. [refseq;acc:nm_006530]	Measured
			Ranked
			Squared
			Rooted
3008	NUP214	nuclear pore complex protein nup214 (nucleoporin nup214) (214 kda nucleoporin) (can protein). [swissprot;acc:p35658]	Measured
			Ranked
			Squared

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.