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 [...,...].

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

Results: HTML CSV LaTeX

Showing element 1968 to 2017 of 3228 in total

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

red	green	Rank	description	network_comparison
5846.67	6269.41	1566	protein phosphatase 1, regulatory (inhibitor) subunit 12b isoform a; myosin phosphatase regulatory subunit; myosin phosphatase, target subunit 2. [refseq;acc:nm_002481]	1.0723
5851.64	6273.4	1571	26s proteasome non-atpase regulatory subunit 7 (26s proteasome regulatory subunit s12) (proteasome subunit p40) (mov34 protein homolog). [swissprot;acc:p51665]	1.07208
5853.1	6271.79	1592	26s proteasome non-atpase regulatory subunit 11 (26s proteasome regulatory subunit s9) (26s proteasome regulatory subunit p44.5). [swissprot;acc:o00231]	1.07153
5853.67	6136.97	2219	arf gtpase-activating protein git1 (g protein-coupled receptor kinase- interactor 1). [swissprot;acc:q9y2x7]	1.0484
5857.48	6380.4	1123	argininosuccinate lyase (ec 4.3.2.1) (arginosuccinase) (asal). [swissprot;acc:p04424]	1.08927
5858.48	6278.32	1585	26s proteasome non-atpase regulatory subunit 13 (26s proteasome regulatory subunit s11) (26s proteasome regulatory subunit p40.5). [swissprot;acc:q9unm6]	1.07166
5859.1	6173.7	2137	sh3 domain-binding glutamic acid-rich protein (sh3bgr protein) (21- glutamic acid-rich protein) (21-garp). [swissprot;acc:p55822]	1.05369
		2138	oxidation resistance 1. [refseq;acc:nm_181354]
		2139	lats, large tumor suppressor, homolog 2; lats (large tumor suppressor, drosophila) homolog 2. [refseq;acc:nm_014572]
		2140	dymeclin. [refseq;acc:nm_017653]
		2141	sh3 domain-binding glutamic acid-rich-like protein. [swissprot;acc:o75368]
		2142	lats homolog 1. [refseq;acc:nm_004690]
		2143	sh3 domain-binding glutamic acid-rich-like protein 2 (fovea-associated sh3 domain binding protein). [swissprot;acc:q9ujc5]
		2144	nuclear receptor coactivator 7; estrogen receptor associated protein 140 kda. [refseq;acc:nm_181782]
		2145	dj132f21.2 (contains a novel protein similar to the l82e from drosophila) (fragment). [sptrembl;acc:q9h125]
		2146	tbc1 domain family protein c22orf4-like (fragment). [swissprot;acc:q9nu19]
		2147	tbc1 domain family protein c22orf4. [swissprot;acc:q8wua7]
5859.25	6432.03	937	nucleobindin 1 precursor (calnuc). [swissprot;acc:q02818]	1.09776
		938	dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692]
		939	nucleobindin 2 precursor (dna-binding protein nefa). [swissprot;acc:p80303]
5864.49	6145.14	2223	abhydrolase domain containing protein 2 (protein phps1-2). [swissprot;acc:p08910]	1.04786
		2224	quaking isoform 6. [sptrembl;acc:q9p0x9]
5865.79	6671.23	549	dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762]	1.13731
5866.19	6245.4	1813	dual specificity mitogen-activated protein kinase kinase 4 (ec 2.7.1.-) (map kinase kinase 4) (jnk activating kinase 1) (c-jun n- terminal kinase kinase 1) (jnkk) (sapk/erk kinase 1) (sek1). [swissprot;acc:p45985]	1.06464
5869.24	6367.8	1232	nuclear factor, interleukin 3 regulated. [refseq;acc:nm_005384]	1.08494
5869.97	6301.24	1528	c1 domain-containing phosphatase and tensin-like protein isoform 2; putative protein tyrosine phosphatase; c1 domain-containing phosphatase and tensin-like protein; tensin 2. [refseq;acc:nm_015319]	1.07347
5870.2	6533.39	760	atpase, h+ transporting, lysosomal 38kda, v0 subunit d isoform 2. [refseq;acc:nm_152565]	1.11298
5870.72	6300.83	1538	tumor endothelial marker 6; thyroid specific ptb domain protein; tensin 3. [refseq;acc:nm_022748]	1.07326
5871.89	6303.56	1525	tensin. [refseq;acc:nm_022648]	1.07351
5873.56	6370.31	1237	tsc22-related inducible leucine zipper protein 2 (tsc-22-like protein thg-1). [swissprot;acc:q9y3q8]	1.08457
		1238	sphingolipid delta 4 desaturase; membrane fatty acid (lipid) desaturase; dihydroceramide desaturase. [refseq;acc:nm_003676]
5873.77	6532.44	769	vacuolar atp synthase subunit f (ec 3.6.3.14) (v-atpase f subunit) (vacuolar proton pump f subunit) (v-atpase 14 kda subunit). [swissprot;acc:q16864]	1.11214
5874.11	6387.23	1174	cda11 protein. [refseq;acc:nm_032026]	1.08735
5874.63	6533.23	778	vacuolar atp synthase subunit b, kidney isoform (ec 3.6.3.14) (v- atpase b1 subunit) (vacuolar proton pump b isoform 1) (endomembrane proton pump 58 kda subunit). [swissprot;acc:p15313]	1.11211
5874.74	6533.33	775	vacuolar atp synthase subunit g 1 (ec 3.6.3.14) (v-atpase g subunit 1) (vacuolar proton pump g subunit 1) (v-atpase 13 kda subunit 1) (vacuolar atp synthase subunit m16). [swissprot;acc:o75348]
		782	vacuolar atp synthase subunit h (ec 3.6.3.14) (v-atpase h subunit) (vacuolar proton pump h subunit) (v-atpase 50/57 kda subunits) (vacuolar proton pump subunit sfd) (cgi-11). [swissprot;acc:q9ui12]
	6533.34	770	vacuolar atp synthase subunit g 2 (ec 3.6.3.14) (v-atpase g subunit 2) (vacuolar proton pump g subunit 2) (v-atpase 13 kda subunit 2). [swissprot;acc:o95670]
		771	apoptosis inhibitor 5; fibroblast growth factor 2-interacting factor 2; api5-like 1. [refseq;acc:nm_006595]
		773	vacuolar atp synthase subunit g 3 (ec 3.6.3.14) (v-atpase g subunit 3) (vacuolar proton pump g subunit 3) (v-atpase 13 kda subunit 3). [swissprot;acc:q96lb4]
		777	dead (asp-glu-ala-asp) box polypeptide 39 isoform 1; nuclear rna helicase, decd variant of dead box family. [refseq;acc:nm_005804]
5874.76	6533.36	772	sec13-related protein. [swissprot;acc:p55735]
		774	yeast sec31p homolog. [refseq;acc:nm_014933]
		776	ganglioside-induced differentiation-associated protein 1-like 1. [refseq;acc:nm_024034]
		779	ganglioside-induced differentiation-associated protein 1. [refseq;acc:nm_018972]
		780	vacuolar atp synthase subunit d (ec 3.6.3.14) (v-atpase d subunit) (vacuolar proton pump d subunit) (v-atpase 28 kda accessory protein). [swissprot;acc:q9y5k8]
		781	secretory pathway component sec31b-1. [refseq;acc:nm_015490]
5874.77		784	vacuolar atp synthase subunit e (ec 3.6.3.14) (v-atpase e subunit) (vacuolar proton pump e subunit) (v-atpase 31 kda subunit) (p31). [swissprot;acc:p36543]	1.1121
5874.78	6533.37	783	vacuolar atp synthase subunit b, brain isoform (ec 3.6.3.14) (v-atpase b2 subunit) (vacuolar proton pump b isoform 2) (endomembrane proton pump 58 kda subunit) (ho57). [swissprot;acc:p21281]
5874.83	6272.26	1733	elongation factor 1-alpha 1 (ef-1-alpha-1) (elongation factor 1 a-1) (eef1a-1) (elongation factor tu) (ef-tu). [swissprot;acc:p04720]	1.06765
		1734	zinc-finger protein zpr1 (zinc finger protein 259). [swissprot;acc:o75312]

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.