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 green red network_comparison

Results: HTML CSV LaTeX

Showing element 351 to 400 of 3228 in total

Value Type	Ranked
Network Comparison Type	Divided
Interaction Map	High confidence
Filtered	1

Rank	description	green	red	network_comparison	
351	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [source:swissprot;acc:o43933]	265.696	242.14	1.09728	
352	protein 1-4 (atp binding protein associated with cell differentiation). [source:swissprot;acc:o14530]	265.696	242.14	1.09728	
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]	211.252	231.73	1.09694	
354	syntaxin 10 (syn10). [source:swissprot;acc:o60499]	257.442	234.691	1.09694	
355	syntaxin 6. [source:swissprot;acc:o43752]	257.414	234.673	1.09691	
356	60s ribosomal protein l10a (csa-19). [source:swissprot;acc:p53025]	266.796	243.24	1.09684	
357	60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [source:swissprot;acc:p27635]	266.661	243.12	1.09683	
358	ribosomal protein l10-like protein. [source:refseq;acc:nm_080746]	266.662	243.12	1.09683	
359	60s ribosomal protein l4 (l1). [source:swissprot;acc:p36578]	262.434	239.277	1.09678	
360	protein transport protein sec61 gamma subunit. [source:swissprot;acc:p38384]	266.559	243.072	1.09663	
361	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [source:refseq;acc:nm_022061]	266.248	242.83	1.09644	
362	apical-like protein (apxl protein). [source:swissprot;acc:q13796]	211.136	231.492	1.09641	
363	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [source:refseq;acc:nm_020859]	211.131	231.481	1.09639	
364	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [source:swissprot;acc:p30876]	266.617	243.208	1.09625	
365	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [source:swissprot;acc:q9p0j6]	266.07	242.744	1.09609	
366	40s ribosomal protein s5. [source:swissprot;acc:p46782]	265.756	242.473	1.09602	
367	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [source:swissprot;acc:p52272]	256.627	234.146	1.09601	
368	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [source:swissprot;acc:q9y606]	265.715	242.66	1.09501	
369	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [source:swissprot;acc:p52815]	265.104	242.159	1.09475	
370	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [source:refseq;acc:nm_031438]	265.104	242.159	1.09475	
371	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [source:refseq;acc:nm_012424]	170.42	186.52	1.09447	
372	ribosomal protein s6 kinase-like 1. [source:refseq;acc:nm_031464]	170.42	186.52	1.09447	
373	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [source:swissprot;acc:q9y3b7]	265.255	242.37	1.09442	
374	transcription factor dp-2 (e2f dimerization partner 2). [source:swissprot;acc:q14188]	244.168	267.208	1.09436	
375	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [source:swissprot;acc:o14802]	265.516	242.686	1.09407	
376	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [source:swissprot;acc:q9ny93]	234.945	257.017	1.09395	
377	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [source:swissprot;acc:o95602]	265.481	242.691	1.09391	
378	60s ribosomal protein l30. [source:swissprot;acc:p04645]	265.365	242.593	1.09387	
379	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [source:swissprot;acc:p54819]	264.163	241.509	1.0938	
380	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [source:refseq;acc:nm_003169]	264.79	242.109	1.09368	
381	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [source:swissprot;acc:q15545]	183.423	200.586	1.09357	
382	tata box binding protein-associated factor, rna polymerase ii, q; taf7-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 50 kd; tbp-associated factor, rna polymerase ii, q. [source:refseq;acc:nm_024885]	183.66	200.791	1.09328	
383	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [source:swissprot;acc:q14498]	217.739	237.862	1.09242	
384	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [source:swissprot;acc:q01094]	244.236	266.421	1.09083	
385	transcription factor e2f2 (e2f-2). [source:swissprot;acc:q14209]	244.236	266.421	1.09083	
386	40s ribosomal protein s14 (pro2640). [source:swissprot;acc:p06366]	264.11	242.238	1.09029	
387	40s ribosomal protein s18 (ke-3) (ke3). [source:swissprot;acc:p25232]	264.11	242.238	1.09029	
388	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	208.756	227.575	1.09015	
389	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [source:swissprot;acc:q15356]	208.756	227.575	1.09015	
390	60s ribosomal protein l13, mitochondrial (l13mt). [source:swissprot;acc:q9byd1]	263.62	241.828	1.09011	
391	40s ribosomal protein s16. [source:swissprot;acc:p17008]	263.62	241.828	1.09011	
392	60s ribosomal protein l13a (23 kda highly basic protein). [source:swissprot;acc:p40429]	263.615	241.83	1.09008	
393	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [source:swissprot;acc:o14834]	207.072	225.719	1.09005	
394	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [source:refseq;acc:nm_139159]	238.407	218.827	1.08948	
395	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [source:refseq;acc:nm_017743]	238.407	218.827	1.08948	
396	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [source:swissprot;acc:o75642]	262.34	240.801	1.08945	
397	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [source:swissprot;acc:p49368]	101.613	110.689	1.08932	
398	muscle-specific beta 1 integrin binding protein. [source:refseq;acc:nm_014446]	238.358	218.818	1.0893	
399	clathrin heavy chain 1 (clh-17). [source:swissprot;acc:q00610]	226.226	207.889	1.08821	
400	phosducin-like protein (phlp). [source:swissprot;acc:q13371]	226.218	207.908	1.08807	

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/