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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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 Rank Value Type description Interaction Map red Network Comparison Type green Filtered network_comparison
Results: HTML CSV LaTeX Showing element 451 to 500 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
red
Network Comparison Type
green
Filtered
network_comparison
113 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] 5673.33 Divided 6797.56 0 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] 194.372 Subtracted 234.204 1 39.832
114 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 37.447
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] 8871.11 Divided 10603.2 0 1.19525
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 332.874 267.246 1 1.24557
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 19355 Subtracted 17469.2 0 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] 11124.8 13005.3 1880.5
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 277.546 240.461 1 37.085
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 332.874 Divided 267.246 1.24557
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 18662.8 15627 0 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] 11123.4 Subtracted 13000.1 1876.7
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] 268.565 Divided 334.483 1 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] 208.52 Subtracted 171.595 36.925
metaxin 1. [swissprot;acc:q13505] 13761.3 Divided 16422.1 0 1.19335
117 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 11545 13771.5 1.19285
block 23. [sptrembl;acc:q8nhw5] 11469.3 Subtracted 13334.8 1865.5
high-mobility group 20a. [refseq;acc:nm_018200] 208.588 171.778 1 36.81
neuralized-like. [refseq;acc:nm_004210] 332.326 Divided 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] 12049 14370.7 0 1.19269
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] 3845 Subtracted 5699 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] 284.753 Divided 228.934 1 1.24382
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 274.027 Subtracted 237.79 36.237
119 adiponectin receptor 2. [refseq;acc:nm_024551] 281.582 246.371 35.211
mesoderm induction early response 1. [refseq;acc:nm_020948] 3609 Divided 4302.5 0 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] 318.982 259.004 1 1.23157
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] 7739.47 Subtracted 9580.95 0 1841.48
120 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 227.199 192.715 1 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] 269.278 Divided 327.709 1.21699
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 5797 4873 0 1.18962
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] 11438 Subtracted 13277.1 1839.1
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 269.254 Divided 327.655 1 1.2169
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] 18241.7 Subtracted 16405 0 1836.7
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 227.202 192.823 1 34.379
zinc finger protein 232. [swissprot;acc:q9uny5] 11523.7 Divided 13686.9 0 1.18772
122 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 199.949 Subtracted 234.187 1 34.238
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 12384.7 10549.4 0 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] 269.248 Divided 327.642 1 1.21688
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 11523 13685.4 0 1.18766
123 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 12335.3 Subtracted 10506.8 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] 269.23 Divided 327.601 1 1.21681
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 227.032 Subtracted 193.056 33.976
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] 11522.8 Divided 13684.9 0 1.18764
124 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] 12328.5 Subtracted 10501 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] 208.52 Divided 171.595 1 1.21519
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 285.684 Subtracted 252.234 33.45
zinc finger imprinted 2. [swissprot;acc:q9nzv7] 11520.7 Divided 13680.4 0 1.18746
125 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 12314.9 Subtracted 10489.3 1825.6
high-mobility group 20a. [refseq;acc:nm_018200] 208.588 Divided 171.778 1 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] 22038 18578 0 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] 285.684 Subtracted 252.234 1 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/