MK5 Microarray Data

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

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Showing element 336 to 385 of 3228 in total

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

Rank	Hugo	description	red	network_comparison	green
336	CDK2AP1	cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519]	312	1.09859	284
337	no value	60s ribosomal protein l12. [swissprot;acc:p30050]	243.583	1.0983	267.527
338		60s ribosomal protein l12 like protein. [sptrembl;acc:o60886]			267.528
339		dj999l4.1 (novel protein similar to ribosomal protein l12 (rpl12)). [sptrembl;acc:q9nq02]			267.527
340	MYEF2	myelin gene expression factor 2. [refseq;acc:nm_016132]	235.383	1.09811	258.476
341	no value	60s ribosomal protein l9. [swissprot;acc:p32969]	240.243	1.09805	263.798
342	RPS20	40s ribosomal protein s20. [swissprot;acc:p17075]	243.5	1.09737	267.21
343	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	241.625	1.0973	265.136
344	no value	40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880]
345	CMPK	ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085]	242.14	1.09729	265.697
346	RPS3	40s ribosomal protein s3. [swissprot;acc:p23396]	241.612		265.119
347	AK3	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	242.14		265.697
348	no value	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]		1.09728	265.696
349	MED22	surfeit locus protein 5. [swissprot;acc:q15528]
350	SCAPER	zinc finger protein 291. [swissprot;acc:q9by12]
351	PEX1	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]
352	TXNDC9	protein 1-4 (atp binding protein associated with cell differentiation). [swissprot;acc:o14530]
353	GIPC1	rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908]	231.73	1.09694	211.252
354	STX10	syntaxin 10 (syn10). [swissprot;acc:o60499]	234.691		257.442
355	STX6	syntaxin 6. [swissprot;acc:o43752]	234.673	1.09691	257.414
356	no value	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	243.24	1.09684	266.796
357		60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12	1.09683	266.661
358	RPL10L	ribosomal protein l10-like protein. [refseq;acc:nm_080746]			266.662
359	RPL4	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	239.277	1.09678	262.434
360	SEC61G	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	243.072	1.09663	266.559
361	MRPL17	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	242.83	1.09644	266.248
362	SHROOM2	apical-like protein (apxl protein). [swissprot;acc:q13796]	231.492	1.09641	211.136
363	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	231.481	1.09639	211.131
364	POLR2B	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	243.208	1.09625	266.617
365	MRPL36	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	242.744	1.09609	266.07
366	RPS5	40s ribosomal protein s5. [swissprot;acc:p46782]	242.473	1.09602	265.756
367	HNRPM	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	234.146	1.09601	256.627
368	PUS1	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	242.66	1.09501	265.715
369	MRPL12	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	242.159	1.09475	265.104
370	NUDT12	nudix (nucleoside diphosphate linked moiety x)-type motif 12. [refseq;acc:nm_031438]
371	RPS6KC1	ribosomal protein s6 kinase, 52kda, polypeptide 1; ribosomal protein s6 kinase, 52kd, polypeptide 1. [refseq;acc:nm_012424]	186.52	1.09447	170.42
372	no value	ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464]
373	MRPL11	60s ribosomal protein l11, mitochondrial precursor (l11mt) (cgi-113). [swissprot;acc:q9y3b7]	242.37	1.09442	265.255
374	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	267.208	1.09436	244.168
375	POLR3A	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	242.686	1.09407	265.516
376	DDX56	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	257.017	1.09395	234.945
377	POLR1A	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	242.691	1.09391	265.481
378	RPL30	60s ribosomal protein l30. [swissprot;acc:p04645]	242.593	1.09387	265.365
379	AK2	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	241.509	1.0938	264.163
380	no value	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	242.109	1.09368	264.79
381	TAF7	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	200.586	1.09357	183.423
382	TAF7L	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. [refseq;acc:nm_024885]	200.791	1.09328	183.66
383	RBM39	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	237.862	1.09242	217.739
384	E2F1	transcription factor e2f1 (e2f-1) (retinoblastoma binding protein 3) (rbbp-3) (prb-binding protein e2f-1) (pbr3) (retinoblastoma-associated protein 1) (rbap-1). [swissprot;acc:q01094]	266.421	1.09083	244.236
385	E2F2	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]

Legend:
- Rank is the rank after comparing the two networks
- Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
- Hugo is the HGNC identifier if it exists
- 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.