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

Results: HTML CSV LaTeX

Showing element 741 to 790 of 29840 in total

Value Type

: Measured
Interaction Map

: High confidence

Rank	description	Network Comparison Type	Filtered	red	green	network_comparison
186	estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454]	Subtracted	0	633.85	460.2	173.65
	eukaryotic translation initiation factor 4 gamma (eif-4-gamma) (eif- 4g) (eif4g) (p220). [swissprot;acc:q04637]	Divided	1	4071.1	5251.75	1.29001
	filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457]	Subtracted	1	4366.44	5899.76	1533.32
	glycine receptor alpha-3 chain precursor. [swissprot;acc:o75311]	Divided	0	470.251	384.733	1.22228
187	dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743]	Subtracted		210.767	384.407	173.64
	importin 9. [refseq;acc:nm_018085]	Divided		1143.55	1397.66	1.22221
	rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]	Subtracted	1	4366.44	5899.76	1533.32
	small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331]	Divided	1	4569.48	5885.79	1.28807
188	nucleosome assembly protein 1-like 4 (nucleosome assembly protein 2) (nap2). [swissprot;acc:q99733]	Divided	0	1143.55	1397.66	1.22221
	protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]	Subtracted	1	4366.44	5899.76	1533.32
	sorcin (22 kda protein) (cp-22) (v19). [swissprot;acc:p30626]	Subtracted	0	1410.81	1582.65	171.84
	source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862]	Divided	1	4571.89	5864.86	1.28281
189	limbic system-associated membrane protein precursor (lsamp). [swissprot;acc:q13449]	Subtracted	0	6830.67	7000.85	170.18
	oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977]	Divided	1	4571.89	5864.86	1.28281
	protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]	Subtracted	1	4366.44	5899.76	1533.32
	pyrroline-5-carboxylate reductase (ec 1.5.1.2) (p5cr) (p5c reductase). [swissprot;acc:p32322]	Divided	0	1249.24	1023.76	1.22025
190	adp-ribosylation factor 3. [swissprot;acc:p16587]	Subtracted	0	300.697	469.346	168.649
	dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656]	Divided	1	4571.89	5864.86	1.28281
	protocadherin 16 precursor (cadherin 19) (cadherin fibroblast 1). [swissprot;acc:q96jq0]	Divided	0	14	11.5	1.21739
	u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]	Subtracted	1	4366.44	5899.76	1533.32
191	60s ribosomal protein l23a. [swissprot;acc:p29316]	Subtracted	0	1295.49	1463.51	168.02
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]	Divided	0	743.066	904.149	1.21678
	filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]	Subtracted	1	4366.44	5899.76	1533.32
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Divided		4638.1	5923.4	1.27712
192	a-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (a-raf-1) (proto-oncogene pks). [swissprot;acc:p10398]	Divided		17757.5	14008	1.26767
	c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02]	Subtracted	0	1295.81	1463.55	167.74
	sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4]	Divided	0	1965.47	2389.69	1.21584
	small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072]	Subtracted	1	10807.4	12338.5	1531.1
193	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333]	Divided	0	23818.1	19621.3	1.21389
	raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (raf-1) (c-raf). [swissprot;acc:p04049]	Divided	1	17756.5	14007.3	1.26766
	serine/threonine protein phosphatase 2a, 65 kda regulatory subunit a, alpha isoform (pp2a, subunit a, pr65-alpha isoform) (pp2a, subunit a, r1-alpha isoform) (medium tumor antigen-associated 61 kda protein). [swissprot;acc:p30153]	Subtracted	1	4612.39	3093.6	1518.79
	transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690]		0	1053.33	887.413	165.917
194	calcyphosine. [swissprot;acc:q13938]		0	472.524	635.875	163.351
	cyclin g2. [swissprot;acc:q16589]	Divided	1	17738.6	13995.7	1.26743
	huntingtin interacting protein c. [refseq;acc:nm_012272]	Subtracted	1	4300.47	5807.72	1507.25
	transcription elongation factor a protein 1 (transcription elongation factor s-ii protein 1) (transcription elongation factor tfiis.o). [swissprot;acc:p23193]	Divided	0	125.5	103.5	1.21256
195	adp-ribosylation factor-like protein 7 (adp-ribosylation factor-like protein lak). [swissprot;acc:p56559]	Divided		23	19	1.21053
	aldehyde dehydrogenase 8 (ec 1.2.1.5). [swissprot;acc:p48448]	Subtracted		1475.05	1312.91	162.14
	cyclin g1 (cyclin g). [swissprot;acc:p51959]	Divided	1	17738.5	13995.6	1.26743
	protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8]	Subtracted		3074.57	4567.51	1492.94
196	aquaporin 4 (wch4) (mercurial-insensitive water channel) (miwc). [swissprot;acc:p55087]	Subtracted		10640.2	12117.8	1477.6
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, epsilon isoform (pp2a, b subunit, b' epsilon isoform) (pp2a, b subunit, b56 epsilon isoform) (pp2a, b subunit, pr61 epsilon isoform) (pp2a, b subunit, r5 epsilon isoform). [swissprot;acc:q16537]	Divided		17738.5	13995.7	1.26742
	t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227]	Divided	0	465.37	562.085	1.20782
	uncharacterized bone marrow protein bm033. [refseq;acc:nm_018452]	Subtracted	0	1475.05	1312.91	162.14
197	aquaporin 5. [swissprot;acc:p55064]		1	10640	12117.6	1477.6
	ba395l14.12 (novel protein similar to small nuclear ribonucleoprotein polypeptide a' (snrpa1)). [sptrembl;acc:q9nu36]		0	743.066	904.149	161.083
	dipeptidyl aminopeptidase-like protein 6 (dipeptidylpeptidase vi) (dipeptidylpeptidase 6) (dipeptidyl peptidase iv like protein) (dipeptidyl aminopeptidase-related protein) (dppx). [swissprot;acc:p42658]	Divided	0	2145.97	1784.22	1.20275
	serine/threonine protein phosphatase 2a, 56 kda regulatory subunit, alpha isoform (pp2a, b subunit, b' alpha isoform) (pp2a, b subunit, b56 alpha isoform) (pp2a, b subunit, pr61 alpha isoform) (pp2a, b subunit, r5 alpha isoform). [swissprot;acc:q15172]	Divided	1	17738.5	13995.7	1.26742
198	aquaporin-cd (aqp-cd) (water channel protein for renal collecting duct) (adh water channel) (aquaporin 2) (collecting duct water channel protein) (wch-cd). [swissprot;acc:p41181]	Subtracted		10639.9	12117.4	1477.5
198	b-raf proto-oncogene serine/threonine-protein kinase (ec 2.7.1.-) (p94) (v-raf murine sarcoma viral oncogene homolog b1). [swissprot;acc:p15056]	Divided		17710.9	13977.7	1.26708

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
- 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/