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	Value Type	description	Interaction Map	Filtered	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 2012 to 2060 of 2060 in total

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

Rank	Hugo	Value Type	description
5049	MAP2K1IP1	Rooted	mitogen-activated protein kinase kinase 1 interacting protein 1 (mek binding partner 1) (mp1) (pro2783). [swissprot;acc:q9uha4]
5050	LPIN2	Measured	lipin 2. [swissprot;acc:q92539]
		Ranked
		Squared
		Rooted
5051	SAMHD1	Measured	sam domain and hd domain-containing protein 1 (dendritic cell-derived ifng-induced protein) (dcip) (monocyte protein 5) (mop-5). [swissprot;acc:q9y3z3]
		Ranked
		Squared
		Rooted
5052	TTLL1	Measured	tubulin tyrosine ligase-like protein 1. [swissprot;acc:o95922]
		Ranked
		Squared
		Rooted
5053	GGTL4	Measured	gamma-glutamyltransferase. [sptrembl;acc:q14390]
		Ranked
		Squared
		Rooted
5054	GGT1	Measured	gamma-glutamyltranspeptidase 1 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 1) (cd224 antigen). [swissprot;acc:p19440]
		Ranked
		Squared
		Rooted
5055	GGTLA1	Measured	gamma-glutamyltranspeptidase 5 precursor (ec 2.3.2.2) (gamma- glutamyltransferase 5) (ggt-rel). [swissprot;acc:p36269]
		Ranked
		Squared
		Rooted
5056	DERL3	Measured	putative nadh oxidoreductase complex i subunit homolog. [sptrembl;acc:q96q80]
		Ranked
		Squared
		Rooted
5057	LRRFIP2	Measured	leucine rich repeat (in flii) interacting protein 2. [refseq;acc:nm_006309]
		Ranked
		Squared
		Rooted
5058	DERL2	Measured	carcinoma related gene. [refseq;acc:nm_016041]
		Ranked
		Squared
		Rooted
5059	CBFB	Measured	core-binding factor, beta subunit (cbf-beta) (polyomavirus enhancer binding protein 2 beta subunit) (pebp2-beta) (pea2-beta) (sl3-3 enhancer factor 1 beta subunit) (sl3/akv core-binding factor beta subunit). [swissprot;acc:q13951]
		Ranked
		Squared
		Rooted
5060	HERPUD1	Measured	homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 1 protein (methyl methanesulfonate (mmf)-inducible fragment protein 1). [swissprot;acc:q15011]
		Ranked
		Squared
		Rooted
5061	RUNX3	Measured	runt-related transcription factor 3 (core-binding factor, alpha 3 subunit) (cbf-alpha 3) (acute myeloid leukemia 2 protein) (oncogene aml-2) (polyomavirus enhancer binding protein 2 alpha c subunit) (pebp2-alpha c) (pea2-alpha c) (sl3-3 enhancer factor 1 alpha c subunit) (sl3/akv core-binding factor alpha c subunit). [swissprot;acc:q13761]
		Ranked
		Squared
		Rooted

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.