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 3080 to 3129 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
385	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]	Ranked	1	266.421	244.236	1.09083
386	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	Ranked		242.238	264.11	1.09029
	60s ribosomal protein l8. [swissprot;acc:p25120]	Measured		4533.74	5279.4	1.16447
	galectin-4 (lactose-binding lectin 4) (l-36 lactose binding protein) (l36lbp) (antigen ny-co-27). [swissprot;acc:p56470]	Rooted	0	39.0883	37.7357	1.03584
	mesoderm induction early response 1. [refseq;acc:nm_020948]	Squared		958.952	880.365	1.08927
	pram-1 protein; pml-rara target gene encoding an adaptor molecule-1. [refseq;acc:nm_032152]	Measured		2156.64	2254.12	1.0452
	protein translation factor sui1 homolog gc20. [swissprot;acc:o60739]	Rooted	1	50.0513	45.4124	1.10215
	scratch; scratch 1. [refseq;acc:nm_031309]	Squared	1	40388.9	49827.5	1.23369
	testis-specific chromodomain y protein 1. [swissprot;acc:q9y6f8]	Ranked	0	10303.7	10687.4	1.03724
387	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]	Ranked	1	242.238	264.11	1.09029
	60s ribosomal protein l14 (cag-isl 7). [swissprot;acc:p50914]	Rooted	1	50.3345	45.6718	1.10209
	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Measured	0	1388.29	1330.37	1.04354
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Squared	1	15053	18568	1.23351
	hepatoma-derived growth factor (hdgf) (high-mobility group protein 1- like 2) (hmg-1l2). [swissprot;acc:p51858]	Measured	1	4533.74	5279.4	1.16447
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Rooted	0	29.6492	28.6255	1.03576
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Squared		12.0783	13.1443	1.08826
	thymidylate kinase (ec 2.7.4.9) (dtmp kinase). [swissprot;acc:p23919]	Ranked		10481.8	10869.5	1.03699
388	dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03]	Squared	1	40315.7	49716.4	1.23318
	peroxisomal 3,2-trans-enoyl-coa isomerase (ec 5.3.3.8) (dodecenoyl-coa delta-isomerase) (d3,d2-enoyl-coa isomerase) (dbi-related protein 1) (drs-1) (hepatocellular carcinoma-associated antigen 88). [swissprot;acc:o75521]	Ranked	0	9953.39	10320.9	1.03692
	protein phosphatase 1, regulatory (inhibitor) subunit 14c; serologically defined breast cancer antigen ny-br-81; pkc-potentiated pp1 inhibitory protein. [refseq;acc:nm_030949]	Rooted		34.4922	35.713	1.03539
	putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544]	Squared		948.513	872.867	1.08666
	pwwp domain containing 1; hdgf (hepatoma-derived growth factor) like. [refseq;acc:nm_138574]	Measured	1	4533.74	5279.4	1.16447
	scratch; scratch 1. [refseq;acc:nm_031309]	Measured	0	1398.21	1339.9	1.04352
	serine racemase (ec 5.1.1.-). [swissprot;acc:q9gzt4]	Rooted	1	50.3345	45.6718	1.10209
	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	Ranked		227.575	208.756	1.09015
389	60s ribosomal protein l34. [swissprot;acc:p49207]	Rooted		50.3345	45.6718	1.10209
	arginyl-trna synthetase-like; arginine-trna ligase. [refseq;acc:nm_020320]	Squared		31819.7	39222.2	1.23264
	homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272]	Ranked	0	11794.7	11375.4	1.03686
	imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549]	Measured		11512.3	12011.7	1.04338
	intersectin 2 (sh3 domain-containing protein 1b) (sh3p18) (sh3p18-like wasp associated protein). [swissprot;acc:q9nzm3]	Rooted		30.454	29.4181	1.03521
	likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745]	Squared		605.501	557.57	1.08596
	probable atp-dependent rna helicase p54 (oncogene rck) (dead-box protein 6). [swissprot;acc:p26196]	Measured	1	4533.74	5279.4	1.16447
	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]	Ranked		227.575	208.756	1.09015
390	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]			241.828	263.62	1.09011
	alpha-nac protein. [sptrembl;acc:q9h009]		0	14204.4	14724.5	1.03662
	alpha-nac protein. [sptrembl;acc:q9h009]	Squared		12.1126	13.1421	1.08499
	microsomal signal peptidase 18 kda subunit (ec 3.4.-.-) (spase 18 kda subunit) (spc18) (endopeptidase sp18). [swissprot;acc:p21378]	Measured		11512.3	12011.7	1.04338
	nuclear receptor co-repressor/hdac3 complex subunit tblr1 (tbl1- related protein 1). [swissprot;acc:q9bzk7]	Squared	1	28895.6	35572.8	1.23108
	protein transport protein sec61 alpha subunit isoform 2 (sec61 alpha- 2). [swissprot;acc:q9y2r3]	Rooted		50.3345	45.6718	1.10209
	rw1 protein (fragment). [swissprot;acc:q92545]	Measured		4533.74	5279.4	1.16447
	williams-beuren syndrome critical region protein 20 copy b. [refseq;acc:nm_145645]	Rooted	0	7.21166	7.46223	1.03475
391	40s ribosomal protein s16. [swissprot;acc:p17008]	Ranked	1	241.828	263.62	1.09011
	importin beta-1 subunit (karyopherin beta-1 subunit) (nuclear factor p97) (importin 90). [swissprot;acc:q14974]	Squared	1	28895.6	35572.8	1.23108
	nascent-polypeptide-associated complex alpha polypeptide. [refseq;acc:nm_005594]	Ranked	0	14223.9	14738.5	1.03618
	nuclear rna export factor 5 (tap-like protein 1) (tapl-1). [swissprot;acc:q9h1b4]	Squared	0	9106.26	9878.65	1.08482
	protein transport protein sec61 alpha subunit isoform 1 (sec61 alpha- 1). [swissprot;acc:p38378]	Rooted	1	50.3345	45.6718	1.10209
	seven in absentia homolog 1. [refseq;acc:nm_003031]	Measured	0	2221.04	2316.94	1.04318
	tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148]	Measured	1	3658.76	3144.39	1.16358
	williams beuren syndrome critical region 20a isoform 2; nol1/nop2/sun gene family member; williams-beuren syndrome critical region protein 20 copy a; williams beuren syndrome chromosome region 20. [refseq;acc:nm_018044]	Rooted	0	7.21166	7.46223	1.03475
392	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	Ranked	1	241.83	263.615	1.09008

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/