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

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Showing element 2708 to 2757 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
339	homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444]	Measured	1	20446.1	24136.4	1.18049
	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]	Squared	1	46785.7	58383.2	1.24789
	keratin associated protein 4-14; keratin associated protein 4.14. [refseq;acc:nm_033059]	Squared	0	3680.04	3222.31	1.14205
	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [refseq;acc:nm_001872]	Rooted	1	77.5797	70.0179	1.108
	tfiih basal transcription factor complex p44 subunit (basic transcription factor 2 44 kda subunit) (btf2-p44) (general transcription factor iih polypeptide 2). [swissprot;acc:q13888]	Ranked	0	10344.1	10903.3	1.05406
340	dystrobrevin binding protein 1; dysbindin. [refseq;acc:nm_032122]	Measured		559.333	600	1.07271
	guanine nucleotide-binding protein g(q), alpha subunit. [swissprot;acc:p50148]	Ranked		11372.3	10792.3	1.05374
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Rooted		29.6283	31.1839	1.0525
	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630]	Measured	1	20446.1	24136.4	1.18049
	keratin associated protein 4.9 (fragment). [sptrembl;acc:q9byq8]	Squared	0	3680.04	3222.31	1.14205
	myelin gene expression factor 2. [refseq;acc:nm_016132]	Ranked	1	235.383	258.476	1.09811
	nuclear matrix protein nmp200 related to splicing factor prp19. [refseq;acc:nm_014502]	Rooted		58.4926	64.8047	1.10791
	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [refseq;acc:nm_015713]	Squared		32117	40054	1.24713
341	60s ribosomal protein l9. [swissprot;acc:p32969]	Ranked		240.243	263.798	1.09805
	ferritin heavy polypeptide-like 17. [swissprot;acc:q9bxu8]	Ranked	0	8702.94	9169.98	1.05366
	folylpolyglutamate synthase, mitochondrial precursor (ec 6.3.2.17) (folylpoly-gamma-glutamate synthetase) (fpgs). [swissprot;acc:q05932]	Measured		6452.66	6019.79	1.07191
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Rooted		29.6311	31.1846	1.05243
	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016]	Measured	1	20446.1	24136.4	1.18049
	keratin associated protein 4-12; keratin associated protein 4.12. [refseq;acc:nm_031854]	Squared	0	3679.97	3222.25	1.14205
	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455]	Rooted	1	51.9812	57.5858	1.10782
	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [swissprot;acc:p23921]	Squared		32056.4	39965.8	1.24673
342	40s ribosomal protein s20. [swissprot;acc:p17075]	Ranked		243.5	267.21	1.09737
	gaba-a receptor-associated protein. [sptrembl;acc:q9by60]	Ranked	0	10074	10609	1.05311
	glutamate dehydrogenase 2, mitochondrial precursor (ec 1.4.1.3) (gdh). [swissprot;acc:p49448]	Measured	0	3691.15	3952.59	1.07083
	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [refseq;acc:nm_004712]	Squared	1	70830.5	56822	1.24653
	histone h2b. [refseq;acc:nm_175055]	Rooted	0	29.6319	31.1848	1.05241
	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067]	Measured	1	20446.1	24136.4	1.18049
	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [swissprot;acc:q99848]	Rooted	1	49.2715	54.5757	1.10765
	star-related lipid transfer protein 6 (stard6) (start domain- containing protein 6). [swissprot;acc:p59095]	Squared	0	3679.95	3222.24	1.14205
343	60s ribosomal protein l17 (l23). [swissprot;acc:p18621]	Rooted	1	50.3169	45.4333	1.10749
	bystin. [swissprot;acc:q13895]	Measured	0	2930.88	3135.76	1.0699
	casein kinase i alpha s-like. [refseq;acc:nm_145203]	Ranked	0	8356.31	8788.62	1.05173
	conserved oligomeric golgi complex component 7. [swissprot;acc:p83436]	Squared	1	70830.5	56822	1.24653
	espin. [refseq;acc:nm_031475]	Squared	0	3679.78	3222.11	1.14204
	histone h2b.e (h2b/e). [swissprot;acc:q99879]	Rooted	0	29.632	31.1848	1.0524
	homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719]	Measured	1	20446.1	24136.4	1.18049
	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	Ranked		241.625	265.136	1.0973
344	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]			241.625	265.136	1.0973
	dihydropyrimidine dehydrogenase [nadp+] precursor (ec 1.3.1.2) (dpd) (dhpdhase) (dihydrouracil dehydrogenase) (dihydrothymine dehydrogenase). [swissprot;acc:q12882]		0	10540.6	10027.6	1.05116
	histone h2b.c (h2b/c). [swissprot;acc:q99880]	Rooted	0	29.633	31.1851	1.05238
	homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056]	Measured	1	20446.1	24136.4	1.18049
	hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597]	Measured	0	2075.64	2220.68	1.06988
	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735]	Squared	1	37226.9	46400.1	1.24641
	keratin associated protein 9-4; keratin associated protein 9.4. [refseq;acc:nm_033191]	Squared	0	3665.1	3211.04	1.14141
	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	Rooted	1	49.4233	54.7327	1.10743
345	alcohol dehydrogenase class iii chi chain (ec 1.1.1.1) (glutathione- dependent formaldehyde dehydrogenase) (ec 1.2.1.1) (fdh). [swissprot;acc:p11766]	Ranked	0	11563.7	12151.8	1.05086
	collagen alpha 5(iv) chain precursor. [swissprot;acc:p29400]	Measured	0	2113.27	2255.28	1.0672
	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143]	Rooted	1	56.2615	62.2958	1.10725
	retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246]	Measured		20446.1	24136.4	1.18049
	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961]	Squared		35793	44595.3	1.24592

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/