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 Interaction Map Network Comparison Type Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
green
red
network_comparison
113 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Divided 0 6797.56 5673.33 1.19816
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] Subtracted 1 234.204 194.372 39.832
114 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 267.265 229.818 37.447
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Divided 0 10603.2 8871.11 1.19525
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 267.246 332.874 1.24557
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 0 17469.2 19355 1885.8
115 dna directed rna polymerase ii polypeptide j-related gene isoform 3; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_032959] 13005.3 11124.8 1880.5
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 1 240.461 277.546 37.085
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 267.246 332.874 1.24557
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 0 15627 18662.8 1.19427
116 dna directed rna polymerase ii polypeptide j-related gene isoform 1; rpb11b1alpha protein; rpb11b1beta; dna-directed rna polymerase ii subunit 11. [refseq;acc:nm_145325] Subtracted 13000.1 11123.4 1876.7
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Divided 1 334.483 268.565 1.24545
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] Subtracted 171.595 208.52 36.925
metaxin 1. [swissprot;acc:q13505] Divided 0 16422.1 13761.3 1.19335
117 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 13771.5 11545 1.19285
block 23. [sptrembl;acc:q8nhw5] Subtracted 13334.8 11469.3 1865.5
high-mobility group 20a. [refseq;acc:nm_018200] 1 171.778 208.588 36.81
neuralized-like. [refseq;acc:nm_004210] Divided 266.948 332.326 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 14370.7 12049 1.19269
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Subtracted 5699 3845 1854
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] Divided 1 228.934 284.753 1.24382
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Subtracted 237.79 274.027 36.237
119 adiponectin receptor 2. [refseq;acc:nm_024551] 246.371 281.582 35.211
mesoderm induction early response 1. [refseq;acc:nm_020948] Divided 0 4302.5 3609 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] 1 259.004 318.982 1.23157
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Subtracted 0 9580.95 7739.47 1841.48
120 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 1 192.715 227.199 34.484
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 327.709 269.278 1.21699
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 0 4873 5797 1.18962
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Subtracted 13277.1 11438 1839.1
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Divided 1 327.655 269.254 1.2169
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Subtracted 0 16405 18241.7 1836.7
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 1 192.823 227.202 34.379
zinc finger protein 232. [swissprot;acc:q9uny5] Divided 0 13686.9 11523.7 1.18772
122 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Subtracted 1 234.187 199.949 34.238
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 0 10549.4 12384.7 1835.3
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] Divided 1 327.642 269.248 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 13685.4 11523 1.18766
123 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Subtracted 10506.8 12335.3 1828.5
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 1 327.601 269.23 1.21681
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 193.056 227.032 33.976
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Divided 0 13684.9 11522.8 1.18764
124 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Subtracted 10501 12328.5 1827.5
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] Divided 1 171.595 208.52 1.21519
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted 252.234 285.684 33.45
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Divided 0 13680.4 11520.7 1.18746
125 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Subtracted 10489.3 12314.9 1825.6
high-mobility group 20a. [refseq;acc:nm_018200] Divided 1 171.778 208.588 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 18578 22038 1.18624
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Subtracted 1 252.234 285.684 33.45

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/