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 red green network_comparison
Results: HTML CSV LaTeX Showing element 708 to 757 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
177 transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Subtracted 1 241.07 267.88 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
integral membrane protein cii-3b. [sptrembl;acc:o75609] 0 14951.6 13204.2 1.13234
transcription factor iiia (factor a) (tfiiia). [swissprot;acc:q92664] Subtracted 10899.5 12217.4 1317.9
179 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 12190.3 13497.2 1306.9
huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] Divided 1 226.884 194.79 1.16476
mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 0 9473.01 10723.7 1.13203
phenylalanine-4-hydroxylase (ec 1.14.16.1) (pah) (phe-4- monooxygenase). [swissprot;acc:p00439] Subtracted 1 227.357 254.15 26.793
180 pp3111 protein. [refseq;acc:nm_022156]
probable calcium-transporting atpase kiaa0703 (ec 3.6.3.8). [swissprot;acc:o75185] 0 7690.02 8991.19 1301.17
rna-binding protein nova-1 (neuro-oncological ventral antigen 1) (onconeural ventral antigen-1) (paraneoplastic ri antigen) (ventral neuron-specific protein 1). [swissprot;acc:p51513] Divided 8407.67 9516.92 1.13193
tar dna-binding protein-43 (tdp-43). [swissprot;acc:q13148] 1 256.228 298.438 1.16474
181 b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] 229.818 267.265 1.16294
importin 7; ran-binding protein 7. [refseq;acc:nm_006391] 0 14864.7 16820.7 1.13159
putative phosphoglycerate mutase 3 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13). [swissprot;acc:q8n0y7] Subtracted 4119 5397 1278
syntaxin 18. [swissprot;acc:q9p2w9] 1 227.357 254.15 26.793
182 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] Divided 277.546 240.461 1.15422
phosphoglycerate mutase 1 (ec 5.4.2.1) (ec 5.4.2.4) (ec 3.1.3.13) (phosphoglycerate mutase isozyme b) (pgam-b) (bpg-dependent pgam 1). [swissprot;acc:p18669] Subtracted 0 4119 5397 1278
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] Divided 11573.8 10231.3 1.13121
rd protein. [swissprot;acc:p18615] Subtracted 1 227.357 254.15 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
dj570f3.6 (novel protein similar to lysophospholipase ii (lypla2)). [sptrembl;acc:q9uge0] Subtracted 0 3859 2582 1277
glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] 1 227.357 254.15 26.793
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] Divided 0 11613 13133.5 1.13093
184 androgen-induced 1; cgi-103 protein; androgen induced protein. [refseq;acc:nm_016108] Subtracted 1 227.357 254.15 26.793
ariadne-2 protein homolog (ari-2) (triad1 protein) (ht005). [swissprot;acc:o95376] 0 3284 4554.5 1270.5
odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] Divided 1 274.027 237.79 1.15239
similar to zinc finger protein 277. [sptrembl;acc:q8wwa6] 0 6279.56 5569.42 1.12751
185 adiponectin receptor 2. [refseq;acc:nm_024551] 1 281.582 246.371 1.14292
atp synthase b chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p24539] Subtracted 227.357 254.15 26.793
ubiquitin-conjugating enzyme e2-18 kda ubch7 (ec 6.3.2.19) (ubiquitin- protein ligase) (ubiquitin carrier protein) (ubcm4) (e2-f1) (l-ubc). [swissprot;acc:p51966] 0 3284 4554.5 1270.5
zinc finger protein 277. [swissprot;acc:q9nrm2] Divided 6279.56 5569.42 1.12751
186 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] 11935.1 10592.8 1.12672
cyclin-dependent kinases regulatory subunit 1 (cks-1) (sid1334) (pnas-16 / pnas-143). [swissprot;acc:p33551] Subtracted 12677.7 13941.7 1264
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 1 226.582 198.444 1.14179
j domain containing protein 1. [swissprot;acc:q9ukb3] Subtracted 227.357 254.15 26.793
187 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Divided 0 9955.22 11213.7 1.12641
rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316] 1 226.582 198.444 1.14179
secreted modular calcium-binding protein 1. [refseq;acc:nm_022137] Subtracted 0 14003.7 12743.3 1260.4
sorting nexin 13 (rgs domain- and phox domain-containing protein) (rgs-px1). [swissprot;acc:q9y5w8] 1 227.357 254.15 26.793
188 60s ribosomal protein l15. [swissprot;acc:p39030] Divided 0 11745.2 13203.1 1.12413
ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Subtracted 1 227.357 254.15 26.793
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
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] Subtracted 0 8409.21 9668.79 1259.58
189 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 9955.22 11213.7 1258.48
cholinephosphate cytidylyltransferase a (ec 2.7.7.15) (phosphorylcholine transferase a) (ctp:phosphocholine cytidylyltransferase a) (ct a) (cct a) (cct-alpha). [swissprot;acc:p49585] 1 241.373 267.352 25.979
protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22] Divided 226.582 198.444 1.14179
sal-like protein 4 (zinc finger protein sall4). [swissprot;acc:q9ujq4] 0 10634.4 9465 1.12355
190 fad synthetase. [refseq;acc:nm_025207] Subtracted 1 241.373 267.352 25.979

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/