Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

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 Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 912 to 961 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
228	sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [source:refseq;acc:nm_005489]	Ranked	226.411	202.088	1.12036	
229	breast cancer antiestrogen resistance 3. [source:refseq;acc:nm_003567]	Ranked	226.401	202.094	1.12028	
229	melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [source:swissprot;acc:p43360]	Rooted	137.446	120.823	1.13758	
229	mitogen-activated protein kinase 12 (ec 2.7.1.37) (extracellular signal-regulated kinase 6) (erk-6) (erk5) (stress-activated protein kinase-3) (mitogen-activated protein kinase p38 gamma) (map kinase p38 gamma). [source:swissprot;acc:p53778]	Squared	42411.6	55802.1	1.31573	
229	myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [source:swissprot;acc:p11055]	Measured	9035	7279.6	1.24114	
230	cysteine-rich protein 1 (crp1) (crp). [source:swissprot;acc:p21291]	Ranked	239.35	267.915	1.11934	
230	myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [source:swissprot;acc:p12882]	Measured	9035	7279.6	1.24114	
230	necdin. [source:swissprot;acc:q99608]	Rooted	137.446	120.823	1.13758	
230	sphingosine kinase 1 (ec 2.7.1.-) (sk 1) (spk 1). [source:swissprot;acc:q9nya1]	Squared	42411.6	55802.1	1.31573	
231	likely ortholog of mouse shc sh2-domain binding protein 1. [source:refseq;acc:nm_024745]	Ranked	239.336	267.881	1.11927	
231	melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [source:swissprot;acc:q9y5v3]	Rooted	137.446	120.823	1.13758	
231	myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [source:swissprot;acc:p12883]	Measured	9035	7279.6	1.24114	
231	udp-n-acetylglucosamine--dolichyl-phosphate n- acetylglucosaminephosphotransferase (ec 2.7.8.15) (gpt) (g1pt) (n-acetylglucosamine-1-phosphate transferase) (glcnac-1-p transferase). [source:swissprot;acc:q9h3h5]	Squared	42411.6	55802.1	1.31573	
232	dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [source:sptrembl;acc:q9h430]	Measured	9035	7279.6	1.24114	
232	melanoma-associated antigen f1 (mage-f1 antigen). [source:swissprot;acc:q9hay2]	Rooted	137.446	120.823	1.13758	
232	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). [source:swissprot;acc:q96qb1]	Squared	42411.6	55802.1	1.31573	
232	smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [source:swissprot;acc:q16527]	Ranked	239.336	267.879	1.11926	
233	lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [source:swissprot;acc:p50461]	Ranked	239.32	267.842	1.11918	
233	map kinase-activated protein kinase 2 (ec 2.7.1.-) (mapk-activated protein kinase 2) (mapkap kinase 2) (mapkapk-2). [source:swissprot;acc:p49137]	Squared	42411.6	55802.1	1.31573	
233	melanoma antigen, family b, 6. [source:refseq;acc:nm_173523]	Rooted	137.446	120.823	1.13758	
233	myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [source:swissprot;acc:q9ukx3]	Measured	9035	7279.6	1.24114	
234	chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [source:swissprot;acc:q9nrg0]	Ranked	287.41	256.835	1.11905	
234	melanoma-associated antigen 4 (mage-4 antigen) (mage-x2) (mage-41). [source:swissprot;acc:p43358]	Rooted	137.446	120.823	1.13758	
234	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [source:swissprot;acc:q15825]	Squared	42411.6	55802.1	1.31573	
234	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	Measured	5181.2	6410.58	1.23728	
235	melanoma-associated antigen 9 (mage-9 antigen). [source:swissprot;acc:p43362]	Rooted	137.446	120.823	1.13758	
235	nitrogen fixation cluster-like. [source:refseq;acc:nm_014301]	Squared	42411.6	55802.1	1.31573	
235	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [source:swissprot;acc:p00439]	Ranked	227.357	254.15	1.11785	
235	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	Measured	5181.2	6410.58	1.23728	
236	melanoma-associated antigen 8 (mage-8 antigen). [source:swissprot;acc:p43361]	Rooted	137.446	120.823	1.13758	
236	pp3111 protein. [source:refseq;acc:nm_022156]	Ranked	227.357	254.15	1.11785	
236	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	Measured	4723.53	5828.46	1.23392	
236	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [source:swissprot;acc:q9y3m8]	Squared	42411.6	55802.1	1.31573	
237	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [source:swissprot;acc:o60732]	Rooted	137.446	120.823	1.13758	
237	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [source:swissprot;acc:q92502]	Squared	42411.6	55802.1	1.31573	
237	syntaxin 18. [source:swissprot;acc:q9p2w9]	Ranked	227.357	254.15	1.11785	
237	u6 snrna-associated sm-like protein lsm5. [source:swissprot;acc:q9y4y9]	Measured	4567.04	5631.2	1.23301	
238	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [source:swissprot;acc:p43365]	Rooted	137.446	120.823	1.13758	
238	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [source:swissprot;acc:q15822]	Squared	42411.6	55802.1	1.31573	
238	protein phosphatase 1, regulatory subunit 7; sds22. [source:refseq;acc:nm_002712]	Measured	27642.5	22440.4	1.23182	
238	rd protein. [source:swissprot;acc:p18615]	Ranked	227.357	254.15	1.11785	
239	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Measured	7711.38	6265.8	1.23071	
239	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [source:swissprot;acc:p78417]	Ranked	227.357	254.15	1.11785	
239	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [source:swissprot;acc:p43355]	Rooted	137.446	120.823	1.13758	
239	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [source:refseq;acc:nm_004635]	Squared	42411.6	55802.1	1.31573	
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [source:refseq;acc:nm_016108]	Ranked	227.357	254.15	1.11785	
240	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Measured	7711.36	6265.79	1.23071	
240	melanoma-associated antigen 10 (mage-10 antigen). [source:swissprot;acc:p43363]	Rooted	137.446	120.823	1.13758	
240	mitogen-activated protein kinase 14 (ec 2.7.1.37) (mitogen-activated protein kinase p38alpha) (map kinase p38alpha) (cytokine suppressive anti-inflammatory drug binding protein) (csaid binding protein) (csbp) (max-interacting protein 2) (map kinase mxi2) (sapk2a). [source:swissprot;acc:q16539]	Squared	42411.6	55802.1	1.31573	
241	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [source:swissprot;acc:p24539]	Ranked	227.357	254.15	1.11785	

Legend:
- Rank is the rank after comparing the two networks
- 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.
- http://analysis.yellowcouch.org/