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 Interaction Map Value Type Network Comparison Type Filtered red network_comparison green
Results: HTML CSV LaTeX Showing element 451 to 500 of 7460 in total
Interaction Map  : High confidence
Value Type  : Ranked
Rank
description
Network Comparison Type
Filtered
red
network_comparison
green
113 segment polarity protein dishevelled homolog dvl-1 (dishevelled-1) (dsh homolog 1). [swissprot;acc:o14640] Divided 0 5673.33 1.19816 6797.56
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 1 194.372 39.832 234.204
114 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 37.447 267.265
bloom's syndrome protein (ec 3.6.1.-) (recq protein-like 3) (dna helicase, recq-like, type 2). [swissprot;acc:p54132] Divided 0 8871.11 1.19525 10603.2
kh domain containing, rna binding, signal transduction associated 1; gap-associated tyrosine phosphoprotein p62 (sam68). [refseq;acc:nm_006559] 1 332.874 1.24557 267.246
lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] Subtracted 0 19355 1885.8 17469.2
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 1880.5 13005.3
histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 1 277.546 37.085 240.461
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 332.874 1.24557 267.246
spir-2 protein (fragment). [sptrembl;acc:q8wwl2] 0 18662.8 1.19427 15627
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 11123.4 1876.7 13000.1
guanine nucleotide-binding protein g(i)/g(s)/g(t) beta subunit 3 (transducin beta chain 3). [swissprot;acc:p16520] Divided 1 268.565 1.24545 334.483
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 208.52 36.925 171.595
metaxin 1. [swissprot;acc:q13505] Divided 0 13761.3 1.19335 16422.1
117 basic proline-rich peptide p-e (ib-9). [swissprot;acc:p02811] 11545 1.19285 13771.5
block 23. [sptrembl;acc:q8nhw5] Subtracted 11469.3 1865.5 13334.8
high-mobility group 20a. [refseq;acc:nm_018200] 1 208.588 36.81 171.778
neuralized-like. [refseq;acc:nm_004210] Divided 332.326 1.24491 266.948
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 1.19269 14370.7
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Subtracted 3845 1854 5699
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 1 284.753 1.24382 228.934
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Subtracted 274.027 36.237 237.79
119 adiponectin receptor 2. [refseq;acc:nm_024551] 281.582 35.211 246.371
mesoderm induction early response 1. [refseq;acc:nm_020948] Divided 0 3609 1.19216 4302.5
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 1.23157 259.004
pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Subtracted 0 7739.47 1841.48 9580.95
120 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 1 227.199 34.484 192.715
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 269.278 1.21699 327.709
presenilin-like protein 1 (ec 3.4.99.-) (sppl2b protein). [swissprot;acc:q8tct7] 0 5797 1.18962 4873
similar to ribosomal protein, large, p0. [sptrembl;acc:q96fq9] Subtracted 11438 1839.1 13277.1
121 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Divided 1 269.254 1.2169 327.655
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] Subtracted 0 18241.7 1836.7 16405
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 1 227.202 34.379 192.823
zinc finger protein 232. [swissprot;acc:q9uny5] Divided 0 11523.7 1.18772 13686.9
122 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Subtracted 1 199.949 34.238 234.187
likely ortholog of rat cytochrome p450 4x1. [refseq;acc:nm_178033] 0 12384.7 1835.3 10549.4
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 1 269.248 1.21688 327.642
zinc finger protein 24 (zinc finger protein 191) (zinc finger protein kox17) (retinoic acid suppression protein a) (rsg-a). [swissprot;acc:p17028] 0 11523 1.18766 13685.4
123 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] Subtracted 12335.3 1828.5 10506.8
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Divided 1 269.23 1.21681 327.601
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Subtracted 227.032 33.976 193.056
zinc finger protein 215 (bwscr2 associated zinc-finger protein 2) (baz 2). [swissprot;acc:q9ul58] Divided 0 11522.8 1.18764 13684.9
124 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Subtracted 12328.5 1827.5 10501
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 1 208.52 1.21519 171.595
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Subtracted 285.684 33.45 252.234
zinc finger imprinted 2. [swissprot;acc:q9nzv7] Divided 0 11520.7 1.18746 13680.4
125 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] Subtracted 12314.9 1825.6 10489.3
high-mobility group 20a. [refseq;acc:nm_018200] Divided 1 208.588 1.21429 171.778
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 1.18624 18578
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 1 285.684 33.45 252.234

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/