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 Network Comparison Type Interaction Map Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 343 to 392 of 6456 in total
Value Type  : Ranked
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
green
red
network_comparison
172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Divided 205.556 174.667 1.17685
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Subtracted 228.752 201.515 27.237
173 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62]
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 193.056 227.032 1.17599
174 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 286 335 1.17133
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Subtracted 200.968 228.1 27.132
175 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Divided 234.187 199.949 1.17123
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Subtracted 201.006 228.085 27.079
176 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Divided 235.908 275.754 1.1689
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Subtracted 244.167 271.016 26.849
177 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided 196.695 229.406 1.1663
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Subtracted 267.88 241.07 26.81
178 density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583]
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 194.72 226.887 1.1652
179 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 194.79 226.884 1.16476
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Subtracted 254.15 227.357 26.793
180 pp3111 protein. [refseq;acc:nm_022156]
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Divided 298.438 256.228 1.16474
181 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 267.265 229.818 1.16294
syntaxin 18. [swissprot;acc:q9p2w9] Subtracted 254.15 227.357 26.793
182 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Divided 240.461 277.546 1.15422
rd protein. [swissprot;acc:p18615] Subtracted 254.15 227.357 26.793
183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided 198.011 228.306 1.153
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Subtracted 254.15 227.357 26.793
184 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108]
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Divided 237.79 274.027 1.15239
185 adiponectin receptor 2. [refseq;acc:nm_024551] 246.371 281.582 1.14292
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Subtracted 254.15 227.357 26.793
186 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] Divided 198.444 226.582 1.14179
j domain containing protein 1. [swissprot;acc:q9ukb3] Subtracted 254.15 227.357 26.793
187 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Divided 198.444 226.582 1.14179
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Subtracted 254.15 227.357 26.793
188 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5]
protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873] Divided 198.444 226.582 1.14179
189 cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] Subtracted 267.352 241.373 25.979
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Divided 198.444 226.582 1.14179
190 fad synthetase. [refseq;acc:nm_025207] Subtracted 267.352 241.373 25.979
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided 198.444 226.582 1.14179
191 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 2 (paps synthethase 2) (papss 2) (sulfurylase kinase 2) (sk2) (sk 2) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o95340] Subtracted 267.352 241.373 25.979
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 198.444 226.582 1.14179
192 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Subtracted 267.352 241.373 25.979
musashi 2 isoform a. [refseq;acc:nm_138962] Divided 199.458 227.491 1.14055
193 bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthethase 1 (paps synthethase 1) (papss 1) (sulfurylase kinase 1) (sk1) (sk 1) [includes: sulfate adenylyltransferase (ec 2.7.7.4) (sulfate adenylate transferase) (sat) (atp-sulfurylase); adenylylsulfate kinase (ec 2.7.1.25) (adenylylsulfate 3'-phosphotransferase) (aps kinase) (adenosine-5'-phosphosulfate 3'-phosphotransferase) (3'- phosphoadenosine-5'-phosphosulfate synthetase)]. [swissprot;acc:o43252] Subtracted 267.352 241.373 25.979
musashi 1. [refseq;acc:nm_002442] Divided 199.458 227.491 1.14055
194 nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Subtracted 267.352 241.373 25.979
nuclear protein ukp68. [refseq;acc:nm_024824] Divided 199.458 227.491 1.14055
195 cholinephosphate cytidylyltransferase b (ec 2.7.7.15) (phosphorylcholine transferase b) (ctp:phosphocholine cytidylyltransferase b) (ct b) (cct b) (cct-beta). [swissprot;acc:q9y5k3] Subtracted 267.352 241.373 25.979
huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 200.417 227.971 1.13748
196 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 231.407 263.215 1.13745
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Subtracted 246.892 272.781 25.889

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/