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	Value Type	Network Comparison Type	Interaction Map	Filtered	green	red	network_comparison

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Showing element 343 to 392 of 3228 in total

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

Rank	Hugo	description	green	red	network_comparison
343	PRMT3	protein arginine n-methyltransferase 3 (ec 2.1.1.-) (fragment). [swissprot;acc:o60678]	265.136	241.625	1.0973
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]	265.697	242.14	1.09729
346	RPS3	40s ribosomal protein s3. [swissprot;acc:p23396]	265.119	241.612
347	AK3	gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7]	265.697	242.14
348	no value	adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144]	265.696		1.09728
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]	211.252	231.73	1.09694
354	STX10	syntaxin 10 (syn10). [swissprot;acc:o60499]	257.442	234.691
355	STX6	syntaxin 6. [swissprot;acc:o43752]	257.414	234.673	1.09691
356	no value	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	266.796	243.24	1.09684
357		60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	266.661	243.12	1.09683
358	RPL10L	ribosomal protein l10-like protein. [refseq;acc:nm_080746]	266.662
359	RPL4	60s ribosomal protein l4 (l1). [swissprot;acc:p36578]	262.434	239.277	1.09678
360	SEC61G	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	266.559	243.072	1.09663
361	MRPL17	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	266.248	242.83	1.09644
362	SHROOM2	apical-like protein (apxl protein). [swissprot;acc:q13796]	211.136	231.492	1.09641
363	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	211.131	231.481	1.09639
364	POLR2B	dna-directed rna polymerase ii 140 kda polypeptide (ec 2.7.7.6) (rna polymerase ii subunit 2) (rpb2). [swissprot;acc:p30876]	266.617	243.208	1.09625
365	MRPL36	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	266.07	242.744	1.09609
366	RPS5	40s ribosomal protein s5. [swissprot;acc:p46782]	265.756	242.473	1.09602
367	HNRPM	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	256.627	234.146	1.09601
368	PUS1	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	265.715	242.66	1.09501
369	MRPL12	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	265.104	242.159	1.09475
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]	170.42	186.52	1.09447
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]	265.255	242.37	1.09442
374	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	244.168	267.208	1.09436
375	POLR3A	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	265.516	242.686	1.09407
376	DDX56	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	234.945	257.017	1.09395
377	POLR1A	dna-directed rna polymerase i largest subunit (ec 2.7.7.6) (rna polymerase i 194 kda subunit) (rpa194). [swissprot;acc:o95602]	265.481	242.691	1.09391
378	RPL30	60s ribosomal protein l30. [swissprot;acc:p04645]	265.365	242.593	1.09387
379	AK2	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	264.163	241.509	1.0938
380	no value	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	264.79	242.109	1.09368
381	TAF7	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	183.423	200.586	1.09357
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]	183.66	200.791	1.09328
383	RBM39	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	217.739	237.862	1.09242
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]	244.236	266.421	1.09083
385	E2F2	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
386	RPS14	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	264.11	242.238	1.09029
387	no value	40s ribosomal protein s18 (ke-3) (ke3). [swissprot;acc:p25232]
388		small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578]	208.756	227.575	1.09015
389	SNRPF	small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356]
390	MRPL13	60s ribosomal protein l13, mitochondrial (l13mt). [swissprot;acc:q9byd1]	263.62	241.828	1.09011
391	RPS16	40s ribosomal protein s16. [swissprot;acc:p17008]
392	RPL13A	60s ribosomal protein l13a (23 kda highly basic protein). [swissprot;acc:p40429]	263.615	241.83	1.09008

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.