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

Results: HTML CSV LaTeX

Showing element 1844 to 1893 of 25824 in total

Interaction Map  : High confidence
Filtered  : 1

Rank	Value Type	Network Comparison Type	description	network_comparison	red	green
231	Ranked	Subtracted	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489]	24.323	226.411	202.088
	Squared	Divided	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	1.31573	42411.6	55802.1
		Subtracted	galectin-9 (hom-hd-21) (ecalectin). [swissprot;acc:o00182]	10788.8	45960.8	56749.6
	Rooted	Divided	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3]	1.13758	137.446	120.823
		Subtracted	myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2]	9.732	95.0526	85.3206
232	Measured	Divided	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	1.24114	9035	7279.6
		Subtracted	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [swissprot;acc:q9h3h5]	1403.89	9649.61	11053.5
	Ranked	Divided	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527]	1.11926	239.336	267.879
		Subtracted	breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567]	24.307	226.401	202.094
	Squared	Divided	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	1.31573	42411.6	55802.1
		Subtracted	c439a6.1 (novel protein similar to heparan sulfate (glucosamine) 3-o- sulfotransferases) (fragment). [sptrembl;acc:q96qi5]	10666.1	41502.9	30836.8
	Rooted	Divided	melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2]	1.13758	137.446	120.823
		Subtracted	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]	9.732	95.0526	85.3206
233	Measured	Divided	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	1.24114	9035	7279.6
		Subtracted	rho-gtpase-activating protein 7 (rho-type gtpase-activating protein 7) (deleted in liver cancer 1 protein) (dlc-1) (hp protein) (star-related lipid transfer protein 12) (stard12) (start domain-containing protein 12). [swissprot;acc:q96qb1]	1403.89	9649.61	11053.5
	Ranked	Divided	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461]	1.11918	239.32	267.842
		Subtracted	60s ribosomal protein l7. [swissprot;acc:p18124]	24.257	235.727	259.984
	Squared	Divided	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	1.31573	42411.6	55802.1
		Subtracted	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3a1; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006042]	10666.1	41502.9	30836.8
	Rooted	Divided	melanoma antigen, family b, 6. [refseq;acc:nm_173523]	1.13758	137.446	120.823
		Subtracted	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882]	9.732	95.0526	85.3206
234	Measured	Divided	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	1.23728	5181.2	6410.58
		Subtracted	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [swissprot;acc:p49137]	1403.89	9649.61	11053.5
	Ranked	Divided	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0]	1.11905	287.41	256.835
		Subtracted	40s ribosomal protein s23. [swissprot;acc:p39028]	24.251	243.944	268.195
	Squared	Divided	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	1.31573	42411.6	55802.1
		Subtracted	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 3b1. [refseq;acc:nm_006041]	10666.1	41502.9	30836.8
	Rooted	Divided	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [swissprot;acc:p43358]	1.13758	137.446	120.823
		Subtracted	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883]	9.732	95.0526	85.3206
235	Measured	Divided	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	1.23728	5181.2	6410.58
		Subtracted	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	1403.89	9649.61	11053.5
	Ranked	Divided	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	1.11785	227.357	254.15
		Subtracted	28s ribosomal protein s12, mitochondrial precursor (mpr-s12) (mt- rps12). [swissprot;acc:o15235]	24.251	243.944	268.195
	Squared	Divided	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	1.31573	42411.6	55802.1
		Subtracted	heparan sulfate d-glucosaminyl 3-o-sulfotransferase 2; heparin-glucosamine 3-o-sulfotransferase. [refseq;acc:nm_006043]	10666.1	41502.9	30836.8
	Rooted	Divided	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	1.13758	137.446	120.823
		Subtracted	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430]	9.732	95.0526	85.3206
236	Measured	Divided	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	1.23392	4723.53	5828.46
		Subtracted	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	1403.89	9649.61	11053.5
	Ranked	Divided	pp3111 protein. [refseq;acc:nm_022156]	1.11785	227.357	254.15
		Subtracted	histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576]	24.224	252.644	228.42
	Squared	Divided	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	1.31573	42411.6	55802.1
		Subtracted	mrna decapping enzyme; histidine triad protein member 5; heat shock-like protein 1. [refseq;acc:nm_014026]	10666.1	41502.9	30836.8
	Rooted	Divided	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	1.13758	137.446	120.823
		Subtracted	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]	9.732	95.0526	85.3206
237	Measured	Divided	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	1.23301	4567.04	5631.2
		Subtracted	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	1403.89	9649.61	11053.5
	Ranked	Divided	syntaxin 18. [swissprot;acc:q9p2w9]	1.11785	227.357	254.15
		Subtracted	mitochondrial 60s ribosomal protein l3 (l3mt). [swissprot;acc:p09001]	24.169	242.011	266.18
	Squared	Divided	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	1.31573	42411.6	55802.1

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
- 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.