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.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

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

Results: HTML CSV LaTeX

Showing element 1868 to 1917 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
234	myosin light chain 1, embryonic muscle/atrial isoform (pro1957). [swissprot;acc:p12829]	Squared	0	5294.83	3966.41	1.33492
	neuronal acetylcholine receptor protein, alpha-6 chain precursor. [swissprot;acc:q15825]	Squared	1	42411.6	55802.1	1.31573
	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	Measured	1	5181.2	6410.58	1.23728
	transcription factor 4 (immunoglobulin transcription factor 2) (itf-2) (sl3-3 enhancer factor 2) (sef-2). [swissprot;acc:p15884]	Ranked	0	16614	18296	1.10124
	wiskott-aldrich syndrome protein family member 3 (wasp-family protein member 3) (verprolin homology domain-containing protein 3). [swissprot;acc:q9upy6]	Measured		5202.89	4550.64	1.14333
235	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	Ranked		14554.5	16027.9	1.10123
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Measured		1612.86	1843.92	1.14326
	melanoma-associated antigen 9 (mage-9 antigen). [swissprot;acc:p43362]	Rooted	1	137.446	120.823	1.13758
	nitrogen fixation cluster-like. [refseq;acc:nm_014301]	Squared		42411.6	55802.1	1.31573
	phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439]	Ranked		227.357	254.15	1.11785
	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]	Measured		5181.2	6410.58	1.23728
	segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640]	Squared	0	23310.5	31089.6	1.33372
	sodium/potassium-transporting atpase alpha-2 chain precursor (ec 3.6.3.9) (sodium pump 2) (na+/k+ atpase 2). [swissprot;acc:p50993]	Rooted	0	26.1597	29.2445	1.11792
236	melanoma-associated antigen 8 (mage-8 antigen). [swissprot;acc:p43361]	Rooted	1	137.446	120.823	1.13758
	peroxisomal acyl-coenzyme a thioester hydrolase 2a (ec 3.1.2.2) (peroxisomal long-chain acyl-coa thioesterase 2) (zap128). [swissprot;acc:p49753]	Measured	0	2715.75	3103.01	1.1426
	pnas-18. [sptrembl;acc:q9bzu3]	Rooted		24.2086	21.6857	1.11634
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Squared		18175.2	13699.8	1.32668
	pp3111 protein. [refseq;acc:nm_022156]	Ranked	1	227.357	254.15	1.11785
	protein phosphatase inhibitor 2 (ipp-2). [swissprot;acc:p41236]	Ranked	0	15245.4	16788.5	1.10122
	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	Measured	1	4723.53	5828.46	1.23392
	star-related lipid transfer protein 13 (stard13) (start domain- containing protein 13) (46h23.2). [swissprot;acc:q9y3m8]	Squared	1	42411.6	55802.1	1.31573
237	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Squared	0	5219.15	3979.89	1.31138
	bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340]	Ranked		9984	9067	1.10114
	dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374]	Rooted		21.2911	23.7622	1.11606
	melanoma-associated antigen c1 (mage-c1 antigen) (cancer-testis antigen ct7). [swissprot;acc:o60732]	Rooted	1	137.446	120.823	1.13758
	p28 ing5. [refseq;acc:nm_032329]	Measured	0	2551.23	2243.69	1.13707
	star-related lipid transfer protein 8 (stard8) (start domain- containing protein 8). [swissprot;acc:q92502]	Squared	1	42411.6	55802.1	1.31573
	syntaxin 18. [swissprot;acc:q9p2w9]	Ranked		227.357	254.15	1.11785
	u6 snrna-associated sm-like protein lsm5. [swissprot;acc:q9y4y9]	Measured		4567.04	5631.2	1.23301
238	casein kinase i alpha s-like. [refseq;acc:nm_145203]	Measured	0	2198.47	1933.94	1.13678
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Ranked		12677.7	13941.7	1.0997
	lipocalin-interacting membrane receptor. [refseq;acc:nm_018113]	Rooted		20.6514	18.5098	1.1157
	melanoma-associated antigen 12 (mage-12 antigen) (mage12f). [swissprot;acc:p43365]	Rooted	1	137.446	120.823	1.13758
	neuronal acetylcholine receptor protein, alpha-2 chain precursor. [swissprot;acc:q15822]	Squared		42411.6	55802.1	1.31573
	protein phosphatase 1, regulatory subunit 7; sds22. [refseq;acc:nm_002712]	Measured		27642.5	22440.4	1.23182
	rd protein. [swissprot;acc:p18615]	Ranked		227.357	254.15	1.11785
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Squared	0	5219.15	3979.89	1.31138
239	carboxypeptidase b precursor. [refseq;acc:nm_020361]	Measured	1	7711.38	6265.8	1.23071
	clathrin heavy chain 2 (clh-22). [swissprot;acc:p53675]	Squared	0	43393.5	56658.6	1.30569
	glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417]	Ranked	1	227.357	254.15	1.11785
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Measured	0	382.142	434.366	1.13666
	melanoma-associated antigen 1 (mage-1 antigen) (antigen mz2-e). [swissprot;acc:p43355]	Rooted	1	137.446	120.823	1.13758
	mitogen-activated protein kinase-activated protein kinase 3; mapkap kinase 3. [refseq;acc:nm_004635]	Squared	1	42411.6	55802.1	1.31573
	mto1 protein homolog (cgi-02). [swissprot;acc:q9y2z2]	Ranked	0	8907.41	9795.36	1.09969
	p28 ing5. [refseq;acc:nm_032329]	Rooted	0	32.711	36.4589	1.11458
240	androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]	Ranked	1	227.357	254.15	1.11785
	integrin beta-3 precursor (platelet membrane glycoprotein iiia) (gpiiia) (cd61 antigen). [swissprot;acc:p05106]	Rooted	0	19.303	21.5023	1.11394
	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [swissprot;acc:p15088]	Measured	1	7711.36	6265.79	1.23071
	melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363]	Rooted	1	137.446	120.823	1.13758
	methyltransferase like 2. [refseq;acc:nm_018396]	Ranked	0	17946	16326	1.09923

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.

- http://analysis.yellowcouch.org/