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.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

value_type as 'ranked' since this provides a very robust analysis method.

intercation map as 'high confidence'

network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins

filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].

Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison

Results: HTML CSV LaTeX

Showing element 1375 to 1424 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	Value Type	red	green	network_comparison	
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	
353	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [source:swissprot;acc:o14908]	Ranked	231.73	211.252	1.09694	
354	paraspeckle protein 1. [source:refseq;acc:nm_018282]	Squared	71360.3	57385.8	1.24352	
354	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	Ranked	234.691	257.442	1.09694	
354	transcription repressor p66 beta component of the mecp1 complex. [source:refseq;acc:nm_020699]	Measured	12839	10911.1	1.17669	
354	wd-repeat protein 12 (ytm1 homolog). [source:swissprot;acc:q9gzl7]	Rooted	49.2848	54.5246	1.10632	
355	enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [source:swissprot;acc:p98073]	Rooted	58.0752	64.23	1.10598	
355	sad1/unc-84 protein-like 1. [source:swissprot;acc:o94901]	Squared	15588.1	19381.8	1.24337	
355	syntaxin 6. [source:swissprot;acc:o43752]	Ranked	234.673	257.414	1.09691	
355	tyrosine aminotransferase (ec 2.6.1.5) (l-tyrosine:2-oxoglutarate aminotransferase) (tat). [source:swissprot;acc:p17735]	Measured	12839	10911.1	1.17669	
356	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	Ranked	243.24	266.796	1.09684	
356	sh3-containing grb2-like protein 3 (sh3 domain protein 2c) (een-b2). [source:swissprot;acc:q99963]	Squared	35247.5	43820.5	1.24322	
356	splicing factor 3b subunit 2 (spliceosome associated protein 145) (sap 145) (sf3b150) (pre-mrna splicing factor sf3b 145 kda subunit). [source:swissprot;acc:q13435]	Rooted	58.0752	64.23	1.10598	
356	t-complex protein 1, alpha subunit (tcp-1-alpha) (cct-alpha). [source:swissprot;acc:p17987]	Measured	11004.2	12944.2	1.1763	

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/