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

Results: HTML CSV LaTeX

Showing element 2051 to 2100 of 12912 in total

Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	Value Type	description	red	green	network_comparison	
513	Squared	transforming protein rhoc (h9). [source:swissprot;acc:p08134]	19987.6	23960.7	1.19878	
513	Rooted	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	51.5881	47.3127	1.09036	
514	Measured	1-acyl-sn-glycerol-3-phosphate acyltransferase delta (ec 2.3.1.51) (1- agp acyltransferase 4) (1-agpat 4) (lysophosphatidic acid acyltransferase-delta) (lpaat-delta) (1-acylglycerol-3-phosphate o- acyltransferase 4). [source:swissprot;acc:q9nrz5]	7477	8532.02	1.1411	
514	Ranked	segment polarity protein dishevelled homolog dvl-2 (dishevelled-2) (dsh homolog 2). [source:swissprot;acc:o14641]	218.613	204.382	1.06963	
514	Squared	thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [source:swissprot;acc:q16762]	19987.6	23960.7	1.19878	
514	Rooted	xpa-binding protein 2 (hcnp protein) (pp3898). [source:swissprot;acc:q9hcs7]	58.7805	64.0772	1.09011	
515	Measured	transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [source:swissprot;acc:q14186]	3890.53	4439.07	1.14099	
515	Ranked	pescadillo homolog 1. [source:swissprot;acc:o00541]	251.297	234.941	1.06962	
515	Squared	3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [source:swissprot;acc:p25325]	19987.6	23960.7	1.19878	
515	Rooted	u6 snrna-associated sm-like protein lsm1 (small nuclear ribonuclear casm) (cancer-associated sm-like). [source:swissprot;acc:o15116]	56.3551	61.4322	1.09009	
516	Measured	n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [source:swissprot;acc:q01415]	4910.6	5600.61	1.14051	
516	Ranked	u6 snrna-associated sm-like protein lsm8. [source:swissprot;acc:o95777]	228.255	213.422	1.0695	
516	Squared	transforming protein rhoa (h12). [source:swissprot;acc:p06749]	19987.6	23960.7	1.19878	
516	Rooted	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	50.7935	46.6042	1.08989	
517	Measured	galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [source:swissprot;acc:p07902]	4910.6	5600.61	1.14051	
517	Ranked	metaxin 2. [source:swissprot;acc:o75431]	219.537	234.793	1.06949	
517	Squared	splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [source:swissprot;acc:q15393]	19263.3	23092.3	1.19877	
517	Rooted	eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [source:swissprot;acc:q13347]	50.0578	54.5502	1.08974	
518	Measured	udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [source:swissprot;acc:q14376]	4910.6	5600.61	1.14051	
518	Ranked	nucleostemin; putative nucleotide binding protein, estradiol-induced. [source:refseq;acc:nm_014366]	250.858	234.563	1.06947	
518	Squared	proline synthetase co-transcribed bacterial homolog protein. [source:swissprot;acc:o94903]	11447.3	13719.2	1.19847	
518	Rooted	trinucleotide repeat containing 15. [source:refseq;acc:nm_015575]	50.0578	54.5502	1.08974	
519	Measured	glycogen [starch] synthase, muscle (ec 2.4.1.11). [source:swissprot;acc:p13807]	9648.27	10994.9	1.13957	
519	Ranked	segment polarity protein dishevelled homolog dvl-3 (dishevelled-3) (dsh homolog 3). [source:swissprot;acc:q92997]	218.702	204.582	1.06902	
519	Squared	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [source:refseq;acc:nm_007195]	22387.1	26827.3	1.19834	
519	Rooted	septin-like protein kiaa0202 (fragment). [source:swissprot;acc:q92599]	114.309	124.527	1.08939	
520	Measured	endo-beta-n-acetylglucosaminidase. [source:refseq;acc:nm_022759]	9642.22	10986.4	1.13941	
520	Ranked	sqv-7-like protein (fragment). [source:sptrembl;acc:o95454]	214.754	229.565	1.06897	
520	Squared	paxillin. [source:swissprot;acc:p49023]	22387.1	26827.3	1.19834	
520	Rooted	breast carcinoma amplified sequence 2; spliceosome associated protein, amplified in breast cancer. [source:refseq;acc:nm_005872]	61.1902	66.6503	1.08923	
521	Measured	u4/u6-associated rna splicing factor. [source:refseq;acc:nm_004698]	5390.78	6142.07	1.13937	
521	Ranked	exosome complex exonuclease rrp41 (ec 3.1.13.-) (ribosomal rna processing protein 41) (p12a). [source:swissprot;acc:q9npd3]	215.237	230.07	1.06891	
521	Squared	carboxypeptidase a5. [source:refseq;acc:nm_080385]	53174	44377.4	1.19822	
521	Rooted	cdc5-like; cdc5 (cell division cycle 5, s. pombe, homolog)-like; cell division cycle 5, s. pombe, homolog-like; cdc5-related protein. [source:refseq;acc:nm_001253]	61.1902	66.6503	1.08923	
522	Measured	glycogen [starch] synthase, liver (ec 2.4.1.11). [source:swissprot;acc:p54840]	9634.98	10976.2	1.1392	
522	Ranked	pleiotropic regulator 1 (prl1homolog, arabidopsis); pleiotropic regulator 1 (prl1, arabidopsis homolog). [source:refseq;acc:nm_002669]	222.893	208.523	1.06891	
522	Squared	carboxypeptidase b precursor (ec 3.4.17.2) (pancreas-specific protein) (pasp). [source:swissprot;acc:p15086]	53174	44377.4	1.19822	
522	Rooted	septin 10 isoform 1. [source:refseq;acc:nm_144710]	113.733	123.871	1.08914	
523	Measured	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [source:swissprot;acc:p55087]	10640.2	12117.8	1.13887	
523	Ranked	exosome complex exonuclease rrp4 (ec 3.1.13.-) (ribosomal rna processing protein 4). [source:swissprot;acc:q13868]	215.237	230.07	1.06891	
523	Squared	neutral and basic amino acid transport protein rbat (b(0,+)-type amino acid transport protein) (nbat) (d2h). [source:swissprot;acc:q07837]	53174	44377.4	1.19822	
523	Rooted	ribonucleoside-diphosphate reductase m1 chain (ec 1.17.4.1) (ribonucleotide reductase large chain). [source:swissprot;acc:p23921]	66.377	72.2842	1.08899	
524	Measured	aquaporin 5. [source:swissprot;acc:p55064]	10640	12117.6	1.13887	
524	Ranked	exosome complex exonuclease rrp40 (ec 3.1.13.-) (ribosomal rna processing protein 40) (p10) (cgi-102). [source:swissprot;acc:q9nqt5]	215.237	230.07	1.06891	
524	Squared	aminoacylase-1 (ec 3.5.1.14) (n-acyl-l-amino-acid amidohydrolase) (acy-1). [source:swissprot;acc:q03154]	53174	44377.4	1.19822	
524	Rooted	brain protein 44. [source:swissprot;acc:o95563]	113.374	123.463	1.08899	
525	Measured	lens fiber major intrinsic protein (mip26) (mp26) (aquaporin 0). [source:swissprot;acc:p30301]	10639.8	12117.3	1.13887	
525	Ranked	exosome complex exonuclease rrp46 (ec 3.1.13.-) (ribosomal rna processing protein 46) (p12b) (chronic myelogenous leukemia tumor antigen 28). [source:swissprot;acc:q9nqt4]	215.237	230.07	1.06891	
525	Squared	carboxypeptidase a1 precursor (ec 3.4.17.1). [source:swissprot;acc:p15085]	53174	44377.4	1.19822	
525	Rooted	septin 7 (cdc10 protein homolog). [source:swissprot;acc:q16181]	113.374	123.463	1.08899	

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/