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.


Navigation/Query Panel:
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 Network Comparison Type Interaction Map Filtered red green 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
red
green
network_comparison
172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Divided 174.667 205.556 1.17685
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Subtracted 201.515 228.752 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 227.032 193.056 1.17599
174 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 335 286 1.17133
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Subtracted 228.1 200.968 27.132
175 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Divided 199.949 234.187 1.17123
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Subtracted 228.085 201.006 27.079
176 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Divided 275.754 235.908 1.1689
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Subtracted 271.016 244.167 26.849
177 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Divided 229.406 196.695 1.1663
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Subtracted 241.07 267.88 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 226.887 194.72 1.1652
179 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 226.884 194.79 1.16476
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Subtracted 227.357 254.15 26.793
180 pp3111 protein. [refseq;acc:nm_022156]
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] Divided 256.228 298.438 1.16474
181 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 1.16294
syntaxin 18. [swissprot;acc:q9p2w9] Subtracted 227.357 254.15 26.793
182 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Divided 277.546 240.461 1.15422
rd protein. [swissprot;acc:p18615] Subtracted 227.357 254.15 26.793
183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] Divided 228.306 198.011 1.153
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Subtracted 227.357 254.15 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 274.027 237.79 1.15239
185 adiponectin receptor 2. [refseq;acc:nm_024551] 281.582 246.371 1.14292
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Subtracted 227.357 254.15 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 226.582 198.444 1.14179
j domain containing protein 1. [swissprot;acc:q9ukb3] Subtracted 227.357 254.15 26.793
187 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] Divided 226.582 198.444 1.14179
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] Subtracted 227.357 254.15 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 226.582 198.444 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 241.373 267.352 25.979
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Divided 226.582 198.444 1.14179
190 fad synthetase. [refseq;acc:nm_025207] Subtracted 241.373 267.352 25.979
u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621] Divided 226.582 198.444 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 241.373 267.352 25.979
filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333] Divided 226.582 198.444 1.14179
192 ligatin (hepatocellular carcinoma-associated antigen 56). [swissprot;acc:p41214] Subtracted 241.373 267.352 25.979
musashi 2 isoform a. [refseq;acc:nm_138962] Divided 227.491 199.458 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 241.373 267.352 25.979
musashi 1. [refseq;acc:nm_002442] Divided 227.491 199.458 1.14055
194 nadph-cytochrome p450 reductase (ec 1.6.2.4) (cpr) (p450r). [swissprot;acc:p16435] Subtracted 241.373 267.352 25.979
nuclear protein ukp68. [refseq;acc:nm_024824] Divided 227.491 199.458 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 241.373 267.352 25.979
huntingtin interacting protein c. [refseq;acc:nm_012272] Divided 227.971 200.417 1.13748
196 forkhead box p4; fork head-related protein like a; winged-helix repressor foxp4. [refseq;acc:nm_138457] 263.215 231.407 1.13745
hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] Subtracted 272.781 246.892 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/