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.

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	Hugo	description	Value Type	Network Comparison Type	Interaction Map	Filtered	red	green	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	Hugo	description	red	green	network_comparison
351	PEX1	peroxisome biogenesis factor 1 (peroxin-1) (peroxisome biogenesis disorder protein 1). [swissprot;acc:o43933]	242.14	265.696	1.09728
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	211.252	1.09694
354	STX10	syntaxin 10 (syn10). [swissprot;acc:o60499]	234.691	257.442
355	STX6	syntaxin 6. [swissprot;acc:o43752]	234.673	257.414	1.09691
356	no value	60s ribosomal protein l10a (csa-19). [swissprot;acc:p53025]	243.24	266.796	1.09684
357		60s ribosomal protein l10 (qm protein) (tumor suppressor qm) (laminin receptor homolog). [swissprot;acc:p27635]	243.12	266.661	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]	239.277	262.434	1.09678
360	SEC61G	protein transport protein sec61 gamma subunit. [swissprot;acc:p38384]	243.072	266.559	1.09663
361	MRPL17	mitochondrial ribosomal protein l17; lyst-interacting protein lip2. [refseq;acc:nm_022061]	242.83	266.248	1.09644
362	SHROOM2	apical-like protein (apxl protein). [swissprot;acc:q13796]	231.492	211.136	1.09641
363	SHROOM3	shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859]	231.481	211.131	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]	243.208	266.617	1.09625
365	MRPL36	60s ribosomal protein l36, mitochondrial precursor (l36mt) (brca1- interacting protein 1). [swissprot;acc:q9p0j6]	242.744	266.07	1.09609
366	RPS5	40s ribosomal protein s5. [swissprot;acc:p46782]	242.473	265.756	1.09602
367	HNRPM	heterogeneous nuclear ribonucleoprotein m (hnrnp m). [swissprot;acc:p52272]	234.146	256.627	1.09601
368	PUS1	trna pseudouridine synthase a (ec 4.2.1.70) (pseudouridylate synthase i) (pseudouridine synthase i) (uracil hydrolyase). [swissprot;acc:q9y606]	242.66	265.715	1.09501
369	MRPL12	60s ribosomal protein l12, mitochondrial precursor (l12mt) (5c5-2). [swissprot;acc:p52815]	242.159	265.104	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]	186.52	170.42	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]	242.37	265.255	1.09442
374	TFDP2	transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188]	267.208	244.168	1.09436
375	POLR3A	dna-directed rna polymerase iii largest subunit (ec 2.7.7.6) (rpc155) (rpc1). [swissprot;acc:o14802]	242.686	265.516	1.09407
376	DDX56	probable atp-dependent 61 kda nucleolar rna helicase (dead-box protein 21). [swissprot;acc:q9ny93]	257.017	234.945	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]	242.691	265.481	1.09391
378	RPL30	60s ribosomal protein l30. [swissprot;acc:p04645]	242.593	265.365	1.09387
379	AK2	adenylate kinase isoenzyme 2, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p54819]	241.509	264.163	1.0938
380	no value	suppressor of ty 5 homolog; suppressor of ty (s.cerevisiae) 5 homolog. [refseq;acc:nm_003169]	242.109	264.79	1.09368
381	TAF7	transcription initiation factor tfiid 55 kda subunit (tafii-55) (tafii55). [swissprot;acc:q15545]	200.586	183.423	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]	200.791	183.66	1.09328
383	RBM39	rna-binding region containing protein 2 (hepatocellular carcinoma protein 1) (splicing factor hcc1). [swissprot;acc:q14498]	237.862	217.739	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]	266.421	244.236	1.09083
385	E2F2	transcription factor e2f2 (e2f-2). [swissprot;acc:q14209]
386	RPS14	40s ribosomal protein s14 (pro2640). [swissprot;acc:p06366]	242.238	264.11	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]	227.575	208.756	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]	241.828	263.62	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]	241.83	263.615	1.09008
393	TXNL4A	spliceosomal u5 snrnp-specific 15 kda protein (dim1 protein homolog) (thioredoxin-like u5 snrnp protein u5-15kd). [swissprot;acc:o14834]	225.719	207.072	1.09005
394	DPP9	dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159]	218.827	238.407	1.08948
395	DPP8	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]
396	no value	putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642]	240.801	262.34	1.08945
397	CCT3	t-complex protein 1, gamma subunit (tcp-1-gamma) (cct-gamma). [swissprot;acc:p49368]	110.689	101.613	1.08932
398	ITGB1BP3	muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446]	218.818	238.358	1.0893
399	CLTC	clathrin heavy chain 1 (clh-17). [swissprot;acc:q00610]	207.889	226.226	1.08821
400	PDCL	phosducin-like protein (phlp). [swissprot;acc:q13371]	207.908	226.218	1.08807

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.