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 description Gene Hugo Network Comparison Type Value Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 275 to 324 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Hugo
Network Comparison Type
red
green
network_comparison
138 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] TIPRL Subtracted 174.667 205.556 30.889
serine/threonine protein phosphatase 2a, catalytic subunit, alpha isoform (ec 3.1.3.16) (pp2a-alpha) (replication protein c) (rp-c). [swissprot;acc:p05323] PPP2CA Divided 194.372 234.204 1.20493
139 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] APBA1 271.752 225.68 1.20415
chromatin accessibility complex protein 1 (chrac-1) (chrac-15) (huchrac15) (dna polymerase epsilon subunit p15). [swissprot;acc:q9nrg0] CHRAC1 Subtracted 287.41 256.835 30.575
140 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] NCBP2 228.306 198.011 30.295
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] RRAGA Divided 59 49 1.20408
141 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] COMP Subtracted 239.991 269.238 29.247
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] RRAGC Divided 59 49 1.20408
142 ras-related gtp binding b short isoform; gtp-binding protein ragb. [refseq;acc:nm_006064] RRAGB
thrombospondin 3 precursor. [swissprot;acc:p49746] THBS3 Subtracted 239.99 269.234 29.244
143 anillin, actin binding protein (scraps homolog, drosophila); anillin (drosophila scraps homolog), actin binding protein. [refseq;acc:nm_018685] ANLN Divided 59 49 1.20408
splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] SF4 Subtracted 240.133 211.382 28.751
144 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] CSRP1 239.35 267.915 28.565
kv channel interacting protein 1; vesicle apc-binding protein; a-type potassium channel modulatory protein 1. [refseq;acc:nm_014592] KCNIP1 Divided 265.686 319.651 1.20312
145 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] SHCBP1 Subtracted 239.336 267.881 28.545
potassium channel-interacting protein 4 isoform 4; calsenilin-like protein. [refseq;acc:nm_147183] KCNIP4 Divided 265.639 319.546 1.20293
146 kv channel interacting protein 2 isoform 4; a-type potassium channel modulatory protein 2; cardiac voltage gated potassium channel modulatory subunit. [refseq;acc:nm_173193] KCNIP2 265.632 319.531 1.20291
smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] CSRP2 Subtracted 239.336 267.879 28.543
147 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] CSRP3 239.32 267.842 28.522
nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [refseq;acc:nm_006333] no value Divided 50.7983 42.3003 1.2009
148 filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] FLNB Subtracted 226.582 198.444 28.138
sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A Divided 296.677 247.559 1.19841
149 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value 142 170 1.19718
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] REV1 Subtracted 226.582 198.444 28.138
150 myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] MYO5B Divided 55 46 1.19565
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] PRMT1 Subtracted 226.582 198.444 28.138
151 myosin vc (myosin 5c). [swissprot;acc:q9nqx4] MYO5C Divided 55 46 1.19565
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] PRMT8 Subtracted 226.582 198.444 28.138
152 myosin va (myosin 5a) (dilute myosin heavy chain, non-muscle) (myosin heavy chain 12) (myoxin). [swissprot;acc:q9y4i1] no value Divided 55 46 1.19565
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] SNRP70 Subtracted 226.582 198.444 28.138
153 chromosome 3p21.1 gene sequence. [refseq;acc:nm_013286] RBM15B Divided 249.663 298.263 1.19466
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] no value Subtracted 226.582 198.444 28.138
154 musashi 2 isoform a. [refseq;acc:nm_138962] MSI2 227.491 199.458 28.033
regulator of g-protein signaling 19 (rgs19) (g-alpha interacting protein) (gaip protein). [swissprot;acc:p49795] RGS19 Divided 249.663 298.263 1.19466
155 musashi 1. [refseq;acc:nm_002442] MSI1 Subtracted 227.491 199.458 28.033
putative rna-binding protein 15 (rna binding motif protein 15) (one-twenty two protein). [swissprot;acc:q96t37] RBM15 Divided 249.663 298.263 1.19466
156 nuclear protein ukp68. [refseq;acc:nm_024824] ZC3H14 Subtracted 227.491 199.458 28.033
regulator of g-protein signaling 20 (rgs20) (regulator of gz- selective protein signaling 1) (gz-selective gtpase-activating protein) (g(z)gap). [swissprot;acc:o76081] RGS20 Divided 249.663 298.263 1.19466
157 neurogenic differentiation factor 2 (neurod2). [swissprot;acc:q15784] NEUROD2 Subtracted 312 284 28
transcription factor lbx1. [swissprot;acc:p52954] LBX1 Divided 249.663 298.263 1.19466
158 chromodomain helicase-dna-binding protein 3 (chd-3) (mi-2 autoantigen 240 kda protein) (mi2-alpha). [swissprot;acc:q12873] CHD3 Subtracted 312 284 28
mosaic protein lgn. [swissprot;acc:p81274] GPSM2 Divided 249.663 298.263 1.19466
159 doc-1 related protein (doc-1r). [swissprot;acc:o75956] CDK2AP2 Subtracted 312 284 28
regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] RGS17 Divided 249.663 298.263 1.19466
160 guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] GNAO1
neurogenic differentiation factor 6 (neurod6) (my051 protein). [swissprot;acc:q96nk8] NEUROD6 Subtracted 312 284 28
161 neurogenic differentiation factor 1 (neurod1) (neurod). [swissprot;acc:q13562] NEUROD1
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] RAP1GAP Divided 249.663 298.263 1.19466
162 atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] no value Subtracted 142 170 28
nostrin. [refseq;acc:nm_052946] NOSTRIN Divided 209.299 249.187 1.19058

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
- Hugo is the HGNC identifier if it exists
- 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/