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 [...,...].
Rank Gene description Value Type Interaction Map Network Comparison Type Filtered green network_comparison red
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
network_comparison
red
113 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Divided 0 6797.56 1.19816 5673.33
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 39.832 194.372
114 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 267.265 37.447 229.818
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 1.19525 8871.11
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 267.246 1.24557 332.874
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 0 17469.2 1885.8 19355
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 1880.5 11124.8
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 1 240.461 37.085 277.546
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 267.246 1.24557 332.874
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 0 15627 1.19427 18662.8
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 1876.7 11123.4
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Divided 1 334.483 1.24545 268.565
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 36.925 208.52
metaxin 1. [swissprot;acc:q13505] Divided 0 16422.1 1.19335 13761.3
117 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 13771.5 1.19285 11545
block 23. [sptrembl;acc:q8nhw5] Subtracted 13334.8 1865.5 11469.3
high-mobility group 20a. [refseq;acc:nm_018200] 1 171.778 36.81 208.588
neuralized-like. [refseq;acc:nm_004210] Divided 266.948 1.24491 332.326
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 1.19269 12049
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Subtracted 5699 1854 3845
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 1.24382 284.753
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Subtracted 237.79 36.237 274.027
119 adiponectin receptor 2. [refseq;acc:nm_024551] 246.371 35.211 281.582
mesoderm induction early response 1. [refseq;acc:nm_020948] Divided 0 4302.5 1.19216 3609
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 1.23157 318.982
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Subtracted 0 9580.95 1841.48 7739.47
120 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 1 192.715 34.484 227.199
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 1.21699 269.278
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 0 4873 1.18962 5797
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Subtracted 13277.1 1839.1 11438
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Divided 1 327.655 1.2169 269.254
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Subtracted 0 16405 1836.7 18241.7
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 1 192.823 34.379 227.202
zinc finger protein 232. [swissprot;acc:q9uny5] Divided 0 13686.9 1.18772 11523.7
122 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Subtracted 1 234.187 34.238 199.949
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 0 10549.4 1835.3 12384.7
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 1.21688 269.248
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 1.18766 11523
123 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Subtracted 10506.8 1828.5 12335.3
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 1.21681 269.23
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 193.056 33.976 227.032
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Divided 0 13684.9 1.18764 11522.8
124 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Subtracted 10501 1827.5 12328.5
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 1.21519 208.52
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted 252.234 33.45 285.684
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Divided 0 13680.4 1.18746 11520.7
125 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Subtracted 10489.3 1825.6 12314.9
high-mobility group 20a. [refseq;acc:nm_018200] Divided 1 171.778 1.21429 208.588
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 1.18624 22038
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 33.45 285.684

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/