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 1330 to 1379 of 12912 in total 
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
333	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Measured	5039.63	5961.83	1.18299	
333	nucleolar gtp-binding protein 1 (chronic renal failure gene protein) (gtp-binding protein ngb). [source:swissprot;acc:q9bze4]	Rooted	49.0526	54.3781	1.10857	
333	nucleotide binding protein 2 (nbp 2). [source:swissprot;acc:q9y5y2]	Squared	14464.3	18142.8	1.25432	
334	ca2+-dependent endoplasmic reticulum nucleoside diphosphatase; apyrase; soluble calcium-activated nucleotidase scan-1. [source:refseq;acc:nm_138793]	Squared	64975.9	81151.2	1.24894	
334	neurogenic differentiation factor 4 (neurod4). [source:swissprot;acc:q9hd90]	Ranked	312	284	1.09859	
334	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	Rooted	58.6096	64.9655	1.10844	
334	septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [source:swissprot;acc:o43236]	Measured	14924.4	17655.2	1.18298	
335	40s ribosomal protein s11. [source:swissprot;acc:p04643]	Rooted	50.4705	45.5342	1.10841	
335	chromodomain helicase dna binding protein 5. [source:refseq;acc:nm_015557]	Ranked	312	284	1.09859	
335	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	Measured	3494.31	4129.6	1.18181	
335	ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [source:refseq;acc:nm_016304]	Squared	30651.3	38253.3	1.24802	
336	60s ribosomal protein l11. [source:swissprot;acc:p39026]	Rooted	50.3167	45.4063	1.10814	
336	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [source:swissprot;acc:o14519]	Ranked	312	284	1.09859	
336	dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [source:swissprot;acc:q9nr33]	Measured	3751.3	4431.34	1.18128	
336	j kappa-recombination signal binding protein (rbp-j kappa). [source:swissprot;acc:q06330]	Squared	46785.7	58383.2	1.24789	
337	60s ribosomal protein l12. [source:swissprot;acc:p30050]	Ranked	243.583	267.527	1.0983	
337	carboxypeptidase b precursor. [source:refseq;acc:nm_020361]	Rooted	77.5801	70.0182	1.108	
337	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Measured	20446.1	24136.4	1.18049	
337	human immunodeficiency virus type i enhancer binding protein 3. [source:refseq;acc:nm_024503]	Squared	46785.7	58383.2	1.24789	
338	60s ribosomal protein l12 like protein. [source:sptrembl;acc:o60886]	Ranked	243.583	267.528	1.0983	
338	homeobox protein hox-b4 (hox-2f) (hox-2.6). [source:swissprot;acc:p17483]	Measured	20446.1	24136.4	1.18049	
338	mast cell carboxypeptidase a precursor (ec 3.4.17.1) (mc-cpa) (carboxypeptidase a3). [source:swissprot;acc:p15088]	Rooted	77.58	70.0181	1.108	
338	zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [source:swissprot;acc:p15822]	Squared	46785.7	58383.2	1.24789	
339	dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [source:sptrembl;acc:q9nq02]	Ranked	243.583	267.527	1.0983	
339	homeobox protein hox-c5 (hox-3d) (cp11). [source:swissprot;acc:q00444]	Measured	20446.1	24136.4	1.18049	
339	human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [source:swissprot;acc:p31629]	Squared	46785.7	58383.2	1.24789	
339	plasma carboxypeptidase b2 isoform a preproprotein; carboxypeptidase u; thrombin-activatable fibrinolysis inhibitor; carboxypeptidase b-like protein; thrombin-activable fibrinolysis inhibitor. [source:refseq;acc:nm_001872]	Rooted	77.5797	70.0179	1.108	
340	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Measured	20446.1	24136.4	1.18049	
340	myelin gene expression factor 2. [source:refseq;acc:nm_016132]	Ranked	235.383	258.476	1.09811	
340	nuclear matrix protein nmp200 related to splicing factor prp19. [source:refseq;acc:nm_014502]	Rooted	58.4926	64.8047	1.10791	
340	ribonucleotide reductase m2 b (tp53 inducible); p53-inducible ribonucleotide reductase small subunit 2 homolog. [source:refseq;acc:nm_015713]	Squared	32117	40054	1.24713	
341	60s ribosomal protein l9. [source:swissprot;acc:p32969]	Ranked	240.243	263.798	1.09805	
341	homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [source:swissprot;acc:p09016]	Measured	20446.1	24136.4	1.18049	
341	lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [source:swissprot;acc:p05455]	Rooted	51.9812	57.5858	1.10782	
341	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	Squared	32056.4	39965.8	1.24673	
342	40s ribosomal protein s20. [source:swissprot;acc:p17075]	Ranked	243.5	267.21	1.09737	
342	hepatocyte growth factor-regulated tyrosine kinase substrate; human growth factor-regulated tyrosine kinase substrate. [source:refseq;acc:nm_004712]	Squared	70830.5	56822	1.24653	
342	homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [source:swissprot;acc:p09067]	Measured	20446.1	24136.4	1.18049	
342	probable rrna processing protein ebp2 (ebna1 binding protein 2) (nucleolar protein p40). [source:swissprot;acc:q99848]	Rooted	49.2715	54.5757	1.10765	
343	60s ribosomal protein l17 (l23). [source:swissprot;acc:p18621]	Rooted	50.3169	45.4333	1.10749	
343	conserved oligomeric golgi complex component 7. [source:swissprot;acc:p83436]	Squared	70830.5	56822	1.24653	
343	homeobox protein hox-a5 (hox-1c). [source:swissprot;acc:p20719]	Measured	20446.1	24136.4	1.18049	
343	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [source:swissprot;acc:o60678]	Ranked	241.625	265.136	1.0973	
344	40s ribosomal protein s2 (s4) (llrep3 protein). [source:swissprot;acc:p15880]	Ranked	241.625	265.136	1.0973	
344	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Measured	20446.1	24136.4	1.18049	
344	isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [source:swissprot;acc:p48735]	Squared	37226.9	46400.1	1.24641	
344	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [source:swissprot;acc:q9nq55]	Rooted	49.4233	54.7327	1.10743	
345	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	Rooted	56.2615	62.2958	1.10725	
345	retinal short-chain dehydrogenase/reductase 3. [source:refseq;acc:nm_016246]	Measured	20446.1	24136.4	1.18049	
345	sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [source:swissprot;acc:q99961]	Squared	35793	44595.3	1.24592	

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/