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 1362 to 1411 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
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	
345	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [source:swissprot;acc:p30085]	Ranked	242.14	265.697	1.09729	
346	40s ribosomal protein s3. [source:swissprot;acc:p23396]	Ranked	241.612	265.119	1.09729	
346	grb2-related adaptor protein. [source:swissprot;acc:q13588]	Rooted	61.4282	68.0107	1.10716	
346	importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [source:swissprot;acc:p55060]	Squared	34018.3	42373	1.24559	
346	septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [source:swissprot;acc:q8wyj6]	Measured	14229.2	16780.7	1.17931	
347	cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [source:refseq;acc:nm_152902]	Rooted	66.4284	60.0004	1.10713	
347	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	Measured	4991.02	5885.09	1.17914	
347	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [source:swissprot;acc:q9uij7]	Ranked	242.14	265.697	1.09729	
347	small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [source:swissprot;acc:p43330]	Squared	16573.6	20637.8	1.24522	
348	ad24 protein. [source:refseq;acc:nm_022451]	Rooted	49.2558	54.5235	1.10695	
348	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p27144]	Ranked	242.14	265.696	1.09728	
348	golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [source:refseq;acc:nm_015530]	Squared	42566.2	52985.3	1.24477	
348	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	Measured	4991.02	5885.09	1.17914	
349	putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [source:swissprot;acc:o43143]	Measured	4714.85	5554.38	1.17806	
349	sh3-containing grb2-like protein 2 (sh3 domain protein 2a) (endophilin 1) (een-b1). [source:swissprot;acc:q99962]	Squared	35533.9	44227	1.24464	
349	surfeit locus protein 5. [source:swissprot;acc:q15528]	Ranked	242.14	265.696	1.09728	
349	u6 snrna-associated sm-like protein lsm4 (glycine-rich protein) (grp). [source:swissprot;acc:q9y4z0]	Rooted	56.0061	61.9704	1.10649	
350	armet protein precursor (arginine-rich protein). [source:swissprot;acc:p55145]	Squared	35508.7	44191.4	1.24452	
350	neuron navigator 2 isoform l; retinoic acid inducible in neuroblastoma; pore membrane and/or filament interacting like protein 2; helicase helad1. [source:refseq;acc:nm_145117]	Rooted	61.3383	67.8668	1.10643	
350	sedlin. [source:swissprot;acc:o14582]	Measured	17396.9	20483.9	1.17745	
350	zinc finger protein 291. [source:swissprot;acc:q9by12]	Ranked	242.14	265.696	1.09728	
351	e2a-pbx1-associated protein; putative 47 kda protein. [source:refseq;acc:nm_020140]	Rooted	61.3352	67.8618	1.10641	
351	histidine decarboxylase (ec 4.1.1.22) (hdc). [source:swissprot;acc:p19113]	Squared	35508.6	44191.3	1.24452	
351	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	Ranked	242.14	265.696	1.09728	
351	synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [source:swissprot;acc:q9y296]	Measured	17396.9	20483.9	1.17745	
352	40s ribosomal protein s28. [source:swissprot;acc:p25112]	Squared	30682.9	38183.6	1.24446	
352	bet3 homolog. [source:swissprot;acc:o43617]	Measured	17396.9	20483.9	1.17745	
352	neuron navigator 1; neuron navigator-1; pore membrane and/or filament interacting like protein 3. [source:refseq;acc:nm_020443]	Rooted	61.3354	67.8621	1.10641	
352	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	Ranked	242.14	265.696	1.09728	
353	54 kda nuclear rna- and dna-binding protein (p54(nrb)) (p54nrb) (55 kda nuclear protein) (nmt55) (non-pou domain-containing octamer- binding protein) (dna-binding p52/p100 complex, 52 kda subunit). [source:swissprot;acc:q15233]	Squared	71383	57399.3	1.24362	
353	neuron navigator 3; pore membrane and/or filament interacting like protein 1; steerin 3. [source:refseq;acc:nm_014903]	Rooted	61.3354	67.8623	1.10641	
353	p66 alpha. [source:refseq;acc:nm_017660]	Measured	12839	10911.1	1.17669	

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/