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

Results: HTML CSV LaTeX

Showing element 1230 to 1279 of 2060 in total

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

description	Value Type	Rank	Hugo
protein kinase c and casein kinase substrate in neurons protein 1. [swissprot;acc:q9by11]	Ranked	3020	PACSIN1
	Squared
	Rooted
protein kinase c and casein kinase substrate in neurons protein 2. [swissprot;acc:q9unf0]	Measured	3142	PACSIN2
	Ranked
	Squared
	Rooted
protein kinase c and casein kinase substrate in neurons protein 3 (sh3 domain-containing protein 6511) (endophilin i). [swissprot;acc:q9uks6]	Measured	2845	PACSIN3
	Ranked
	Squared
	Rooted
protein kinase c, delta type (ec 2.7.1.-) (npkc-delta). [swissprot;acc:q05655]	Measured	2857	PRKCD
	Ranked
	Squared
	Rooted
protein kinase c, theta type (ec 2.7.1.-) (npkc-theta). [swissprot;acc:q04759]	Measured	3186	PRKCQ
	Ranked
	Squared
	Rooted
protein transport protein sec23a (sec23-related protein a). [swissprot;acc:q15436]	Measured	3135	SEC23A
	Ranked
	Squared
	Rooted
protein transport protein sec23b (sec23-related protein b). [swissprot;acc:q15437]	Measured	3127	SEC23B
	Ranked
	Squared
	Rooted
protein transport protein sec24a (sec24-related protein a) (fragment). [swissprot;acc:o95486]	Measured	3056	SEC24A
	Ranked
	Squared
	Rooted
protein transport protein sec24b (sec24-related protein b). [swissprot;acc:o95487]	Measured	2956	SEC24B
	Ranked
	Squared
	Rooted
protein transport protein sec24c (sec24-related protein c). [swissprot;acc:p53992]	Measured	2910	no value
	Ranked
	Squared
	Rooted
protein transport protein sec24d (sec24-related protein d). [swissprot;acc:o94855]	Measured	2903	SEC24D
	Ranked
	Squared
	Rooted
protein-tyrosine phosphatase, non-receptor type 11 (ec 3.1.3.48) (protein-tyrosine phosphatase 2c) (ptp-2c) (ptp-1d) (sh-ptp3) (sh- ptp2) (shp-2). [swissprot;acc:q06124]	Measured	2789	PTPN11
	Ranked
	Squared
	Rooted
protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Measured	2838	DCHS1
	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.