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 1894 to 1943 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
237	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
	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). [swissprot;acc:q16539]	Squared	1	42411.6	55802.1	1.31573
	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	Measured	0	1475.83	1676.18	1.13575
	rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513]	Squared		7071.05	5421.2	1.30433
241	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]	Squared		4734.34	6172.1	1.30369
	atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539]	Ranked	1	227.357	254.15	1.11785
	fos-related antigen 2. [swissprot;acc:p15408]	Rooted	0	44.3292	39.9005	1.11099
	keratin associated protein 9.2. [refseq;acc:nm_031961]	Measured	0	1225.47	1079.01	1.13574
	melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366]	Rooted	1	137.446	120.823	1.13758
	neuronal acetylcholine receptor protein, alpha-4 chain precursor. [swissprot;acc:p43681]	Squared		42411.6	55802.1	1.31573
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Measured		7711.31	6265.76	1.23071
	secreted modular calcium-binding protein 1. [refseq;acc:nm_022137]	Ranked	0	14003.7	12743.3	1.09891
242	1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446]	Ranked		15260.6	13895.8	1.09822
	cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551]	Rooted		23.9664	21.5733	1.11093
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Squared		21584.2	16770.2	1.28706
	j domain containing protein 1. [swissprot;acc:q9ukb3]	Ranked	1	227.357	254.15	1.11785
	max protein. [swissprot;acc:p25912]	Measured		4640.26	5704.87	1.22943
	melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1]	Rooted		137.446	120.823	1.13758
	neuronal acetylcholine receptor protein, alpha-3 chain precursor. [swissprot;acc:p32297]	Squared		42411.6	55802.1	1.31573
	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393]	Measured	0	729.216	642.343	1.13524
243	alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298]	Rooted	0	28.4971	25.6518	1.11092
	homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839]	Measured	1	4246.95	5208.98	1.22652
	keratin associated protein 4.3 (fragment). [sptrembl;acc:q9byr4]	Measured	0	1225.09	1079.36	1.13502
	phospholipid scramblase 3 (pl scramblase 3) (ca(2+)-dependent phospholipid scramblase 3). [swissprot;acc:q9nry6]	Squared		8335.79	6506.81	1.28109
	polyadenylate-binding protein 3 (poly(a)-binding protein 3) (pabp 3) (testis-specific poly(a)-binding protein). [swissprot;acc:q9h361]	Ranked		1251	1373	1.09752
	sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8]	Ranked	1	227.357	254.15	1.11785
	sphingosine kinase 2 (ec 2.7.1.-) (sk 2) (spk 2). [swissprot;acc:q9nra0]	Squared	1	42411.6	55802.1	1.31573

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/