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 227 to 276 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
114 bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 0 8871.11 10603.2 1.19525
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 332.874 267.246 1.24557
115 kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688]
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 0 18662.8 15627 1.19427
116 guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 1 268.565 334.483 1.24545
metaxin 1. [swissprot;acc:q13505] 0 13761.3 16422.1 1.19335
117 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 11545 13771.5 1.19285
neuralized-like. [refseq;acc:nm_004210] 1 332.326 266.948 1.24491
118 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] 0 12049 14370.7 1.19269
nadh-ubiquinone oxidoreductase subunit b17.2 (ec 1.6.5.3) (ec 1.6.99.3) (complex i-b17.2) (ci-b17.2) (cib17.2) (13 kda differentiation-associated protein). [swissprot;acc:q9ui09] 1 284.753 228.934 1.24382
119 mesoderm induction early response 1. [refseq;acc:nm_020948] 0 3609 4302.5 1.19216
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] 1 318.982 259.004 1.23157
120 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 269.278 327.709 1.21699
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 0 5797 4873 1.18962
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 1 269.254 327.655 1.2169
zinc finger protein 232. [swissprot;acc:q9uny5] 0 11523.7 13686.9 1.18772
122 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] 1 269.248 327.642 1.21688
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 0 11523 13685.4 1.18766
123 potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] 1 269.23 327.601 1.21681
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 0 11522.8 13684.9 1.18764
124 high-mobility group 20b; sox-like transcriptional factor; swi/snf-related matrix-associated actin-dependent regulator of chromatin subfamily e, member 1-related. [refseq;acc:nm_006339] 1 208.52 171.595 1.21519
zinc finger imprinted 2. [swissprot;acc:q9nzv7] 0 11520.7 13680.4 1.18746
125 high-mobility group 20a. [refseq;acc:nm_018200] 1 208.588 171.778 1.21429
phosphatidylinositol-4-phosphate 3-kinase c2 domain-containing beta polypeptide (ec 2.7.1.154) (phosphoinositide 3-kinase-c2-beta) (ptdins-3-kinase c2 beta) (pi3k-c2beta) (c2-pi3k). [swissprot;acc:o00750] 0 22038 18578 1.18624
126 associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 1 94 114 1.21277
ret finger protein 2 (leukemia associated protein 5) (b-cell chronic lymphocytic leukemia tumor suppressor leu5) (putative tumor suppressor rfp2) (tripartite motif protein 13). [swissprot;acc:o60858] 0 9722.71 11493.8 1.18216
127 putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 1 94 114 1.21277
trans-prenyltransferase; polyprenyl pyrophosphate synthetase. [refseq;acc:nm_014317] 0 9411.34 11119.7 1.18152
128 60s ribosomal protein l39. [swissprot;acc:p02404] 11564.4 9794.29 1.18073
associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 1 94 114 1.21277
129 isoleucyl-trna synthetase, cytoplasmic (ec 6.1.1.5) (isoleucine--trna ligase) (ilers) (irs). [swissprot;acc:p41252] 0 14222.5 12058.6 1.17945
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 1 94 114 1.21277
130 enigma protein; lim domain protein. [refseq;acc:nm_005451] 0 14476.2 17069.5 1.17914
protein hspc134 (protein cda04). [swissprot;acc:q9by43] 1 94 114 1.21277
131 dna mismatch repair protein mlh1 (mutl protein homolog 1). [swissprot;acc:p40692] 0 8375.43 9873.58 1.17887
son protein (son3) (negative regulatory element-binding protein) (nre- binding protein) (dbp-5) (bax antagonist selected in saccharomyces 1) (bass1) (protein c21orf50). [swissprot;acc:p18583] 1 294.053 242.562 1.21228
132 rna helicase-related protein; rna helicase-like protein; sf3b125 dead-box protein. [refseq;acc:nm_007372] 0 19048 22389 1.1754
tob2 protein (transducer of erbb-2 2). [swissprot;acc:q14106] 1 350 290 1.2069
133 alpha-parvin (calponin-like integrin-linked kinase binding protein) (ch-ilkbp). [swissprot;acc:q9nvd7] 0 6814 8009 1.17537
tob1 protein (transducer of erbb-2 1). [swissprot;acc:p50616] 1 350 290 1.2069
134 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 0 12314.9 10489.3 1.17404
dab2 interacting protein; ngap-like protein; doc-2/dab2 interactive protein. [refseq;acc:nm_032552] 1 350 290 1.2069
135 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 0 12314.9 10489.3 1.17404
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] 1 350 290 1.2069
136 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 0 12335.3 10506.8 1.17403
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 1 350 290 1.2069
137 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 0 12328.5 10501 1.17403
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 1 350 290 1.2069
138 likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 0 12384.7 10549.4 1.17397
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] 1 194.372 234.204 1.20493

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/