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 red green network_comparison

Results: HTML CSV LaTeX

Showing element 3458 to 3507 of 14920 in total

Network Comparison Type

: Divided
Interaction Map

: High confidence

Rank	description	Value Type	Filtered	red	green	network_comparison
433	laminin gamma-1 chain precursor (laminin b2 chain). [swissprot;acc:p11047]	Rooted	1	54.4927	49.6125	1.09837
	mitochondrial processing peptidase alpha subunit, mitochondrial precursor (ec 3.4.24.64) (alpha-mpp) (p-55) (ha1523). [swissprot;acc:q10713]	Measured	1	5244.88	6036.38	1.15091
	my016 protein. [sptrembl;acc:q9h3k6]	Squared	0	1279.28	1234.42	1.03634
	programmed cell death protein 8, mitochondrial precursor (ec 1.-.-.-) (apoptosis-inducing factor). [swissprot;acc:o95831]	Ranked	1	212.547	229.411	1.07934
	rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150]	Rooted	0	13.7373	13.373	1.02724
	sh3 adapter protein spin90 (sh3 protein interacting with nck, 90 kda) (vaca-interacting protein, 54 kda) (vip54) (af3p21) (diaphanous protein interacting protein) (dia interacting protein-1) (dip-1). [swissprot;acc:q9nzq3]	Measured		100.5	103.25	1.02736
	trinucleotide repeat containing 15. [refseq;acc:nm_015575]	Ranked		772	754	1.02387
434	cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614]	Rooted		14.6265	15.0206	1.02694
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Ranked		10028.5	10261.5	1.02323
	splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533]	Squared	1	18306.1	22230.6	1.21438
	t-box transcription factor tbx6 (t-box protein 6). [swissprot;acc:o95947]	Ranked	1	212.547	229.411	1.07934
	testis-specific protein tpx-1 precursor (cysteine-rich secretory protein-2) (crisp-2). [swissprot;acc:p16562]	Measured	0	201	206.5	1.02736
	thymic stromal co-transporter. [refseq;acc:nm_033051]	Rooted	1	54.4927	49.6125	1.09837
	ubiquinol-cytochrome c reductase complex core protein i, mitochondrial precursor (ec 1.10.2.2). [swissprot;acc:p31930]	Measured	1	5246.38	6037.37	1.15077
	zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028]	Squared	0	3778.25	3909.18	1.03465
435	60s ribosomal protein l19. [swissprot;acc:p14118]	Rooted	1	50.832	46.3081	1.09769
	cytochrome b5 reductase b5r.2. [refseq;acc:nm_016229]	Squared	1	26598.9	32283.5	1.21372
	elav-like protein 3 (hu-antigen c) (huc) (paraneoplastic cerebellar degeneration-associated antigen) (paraneoplastic limbic encephalitis antigen 21). [swissprot;acc:q14576]	Measured	0	5891.28	5737.71	1.02677
	histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]	Ranked		8770.94	8574.04	1.02296
	neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004]	Rooted		14.6265	15.0206	1.02694
	polymerase (dna directed) iota; rad30 (s. cerevisiae) homolog b; polymerase (dna-directed), iota. [refseq;acc:nm_007195]	Ranked	1	221.522	205.286	1.07909
	proline synthetase co-transcribed bacterial homolog protein. [swissprot;acc:o94903]	Measured	1	5233.86	6022.6	1.1507
	zinc finger protein 232. [swissprot;acc:q9uny5]	Squared	0	3778.04	3908.95	1.03465
436	alpha-nac protein. [sptrembl;acc:q9h009]	Measured	0	147.221	151.122	1.0265
	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	Measured	1	6230.94	7168.2	1.15042
	cytochrome b5 reductase 1 (b5r.1). [refseq;acc:nm_016243]	Squared	1	26598.9	32283.5	1.21372
	histone h2b.d (h2b/d). [swissprot;acc:q99877]	Ranked	0	8770.82	8574.19	1.02293
	paxillin. [swissprot;acc:p49023]	Ranked	1	221.522	205.286	1.07909
	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [refseq;acc:nm_016172]	Rooted	1	210.928	192.165	1.09764
	transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594]	Rooted	0	14.6265	15.0206	1.02694
	zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58]	Squared		3778.33	3909.26	1.03465
437	block 23. [sptrembl;acc:q8nhw5]	Rooted		22.6329	22.0536	1.02627
	cdc42-interacting protein 4 (thyroid receptor interacting protein 10) (trip-10). [swissprot;acc:q15642]	Ranked	1	209.921	226.459	1.07878
	histone h2b.s (h2b/s). [swissprot;acc:p57053]	Ranked	0	8770.41	8574.66	1.02283
	nadh-cytochrome b5 reductase (ec 1.6.2.2) (b5r). [swissprot;acc:p00387]	Squared	1	26598.9	32283.5	1.21372
	protein cgi-140 (protein ptd008) (my006 protein). [swissprot;acc:q9y284]	Measured	0	2331	2390	1.02531
	suppressor of swi4 1 homolog (ssf-1) (peter pan homolog). [swissprot;acc:q9nq55]	Measured	1	3779.92	4348.48	1.15042
	zinc finger imprinted 2. [swissprot;acc:q9nzv7]	Squared	0	3779	3909.95	1.03465
	zinc finger protein t86. [swissprot;acc:o00488]	Rooted	1	51.0466	56.024	1.09751
438	3 beta-hydroxysteroid dehydrogenase (fragments). [sptrembl;acc:q9udk8]	Rooted	0	43.8864	44.9836	1.025
	3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362]	Measured	0	2925.57	2853.65	1.0252
	arg/abl-interacting protein 2 isoform 2; arg binding protein 2. [refseq;acc:nm_021069]	Squared	1	28863.2	35031.5	1.21371
	bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817]	Rooted	1	55.1867	60.5522	1.09722
	histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]	Ranked	0	7759.36	7586.42	1.0228
	integral membrane protein cii-3b. [sptrembl;acc:o75609]	Squared	0	15669.3	16209.3	1.03446
	n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227]	Ranked	1	233.723	216.674	1.07869
	swi/snf-related, matrix-associated, actin-dependent regulator of chromatin subfamily f member 1 (swi-snf complex protein p270) (b120). [swissprot;acc:o14497]	Measured		6252.58	7192.88	1.15039
439	40s ribosomal protein s9. [swissprot;acc:p46781]	Ranked		238.986	257.784	1.07866
	cell division cycle protein 23; anaphase-promoting complex subunit 8. [refseq;acc:nm_004661]	Squared		51616.7	42588.9	1.21198
	dok-like protein. [refseq;acc:nm_024872]	Rooted		63.2134	69.352	1.09711

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/