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	red	network_comparison	green

Results: HTML CSV LaTeX

Showing element 1891 to 1940 of 2060 in total

Network Comparison Type  : Subtracted
Filtered  : 1
red  : 0
network_comparison  : 0
green  : 0

Rank	Hugo	description	Value Type	Interaction Map
3228	SCYL3	ezrin-binding partner pace-1 isoform 1. [refseq;acc:nm_020423]	Squared	High confidence
			Rooted
5019	JRKL	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]	Ranked	Low confidence
5020	no value	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]
	JRKL	jerky protein homolog like (hhmjg). [swissprot;acc:q9y4a0]	Measured
			Squared
			Rooted
5021	no value	gamma-glutamyltranspeptidase 2 (ec 2.3.2.2) (gamma-glutamyltransferase 2) (fragment). [swissprot;acc:p36268]	Measured
			Squared
			Rooted
	HDAC3	histone deacetylase 3 (hd3) (rpd3-2). [swissprot;acc:o15379]	Ranked
5022			Measured
			Squared
			Rooted
	TIGD1	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Ranked
5023	SPNS1	spinster-like protein. [sptrembl;acc:q9h2v7]
	TIGD1	tigger transposable element derived 1; jerky (mouse) homolog-like. [refseq;acc:nm_145702]	Measured
			Squared
			Rooted
5024	SPNS1	spinster-like protein. [sptrembl;acc:q9h2v7]	Measured
			Squared
			Rooted
	TK2	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]	Ranked
5025	TIGD6	tigger transposable element derived 6. [refseq;acc:nm_030953]
	TK2	thymidine kinase 2, mitochondrial precursor (ec 2.7.1.21) (mt-tk). [swissprot;acc:o00142]	Measured
			Squared
			Rooted
5026	RUNX1	runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196]	Ranked
	TIGD6	tigger transposable element derived 6. [refseq;acc:nm_030953]	Measured
			Squared
			Rooted
5027	COLEC12	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [refseq;acc:nm_130386]	Ranked
	RUNX1	runt-related transcription factor 1 (core-binding factor, alpha 2 subunit) (cbf-alpha 2) (acute myeloid leukemia 1 protein) (oncogene aml-1) (polyomavirus enhancer binding protein 2 alpha b subunit) (pebp2-alpha b) (pea2-alpha b) (sl3-3 enhancer factor 1 alpha b subunit) (sl3/akv core-binding factor alpha b subunit). [swissprot;acc:q01196]	Measured
			Squared
			Rooted
5028	CLEC4F	likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [refseq;acc:nm_173535]	Ranked
	COLEC12	collectin sub-family member 12 isoform i; scavenger receptor with c-type lectin; collectin placenta 1; scavenger receptor class a, member 4. [refseq;acc:nm_130386]	Measured
			Squared
			Rooted
5029	CLEC4F	likely ortholog of mouse c-type (calcium dependent, carbohydrate recognition domain) lectin, superfamily member 13; c-type lectin 13; likely ortholog of rat kupffer cell c-type lectin receptor. [refseq;acc:nm_173535]	Measured
			Squared
			Rooted
	GGTLA4	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	Ranked
5030	CBWD1	cobw-like protein. [refseq;acc:nm_018491]
	GGTLA4	gamma-glutamyltransferase-like activity 4; gamma-glutamyltranspeptidase-like. [refseq;acc:nm_080920]	Measured
			Squared
			Rooted
5031	CBWD1	cobw-like protein. [refseq;acc:nm_018491]	Measured
			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.