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 318 to 367 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
159 regulator of g-protein signaling 17 (rgs17). [swissprot;acc:q9ugc6] 1 249.663 298.263 1.19466
160 ccr4-not transcription complex, subunit 7 (ccr4-associated factor 1) (caf1) (btg1 binding factor 1). [swissprot;acc:q9uiv1] 0 11732 13530.6 1.15331
guanine nucleotide-binding protein g(o), alpha subunit 1. [swissprot;acc:p09471] 1 249.663 298.263 1.19466
161 cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [refseq;acc:nm_052936] 0 5781.93 6660.63 1.15197
rap1 gtpase-activating protein 1 (rap1gap). [swissprot;acc:p47736] 1 249.663 298.263 1.19466
162 nostrin. [refseq;acc:nm_052946] 209.299 249.187 1.19058
putative eukaryotic translation initiation factor 1a (eif-1a) (eif- 4c). [swissprot;acc:o75642] 0 12301.4 10680.5 1.15176
163 eap30 subunit of ell complex. [refseq;acc:nm_007241] 1 209.299 249.187 1.19058
transcription factor cp2; transcription factor cp2, alpha globin. [refseq;acc:nm_005653] 0 8409.21 9668.79 1.14979
164 dihydrofolate reductase (ec 1.5.1.3). [swissprot;acc:p00374] 11971.7 10412.4 1.14975
liv-1 protein, estrogen regulated. [refseq;acc:nm_012319] 1 209.299 249.187 1.19058
165 glutamate decarboxylase, 65 kda isoform (ec 4.1.1.15) (gad-65) (65 kda glutamic acid decarboxylase). [swissprot;acc:q05329]
ribose-phosphate pyrophosphokinase iii (ec 2.7.6.1) (phosphoribosyl pyrophosphate synthetase iii) (prs-iii). [swissprot;acc:p21108] 0 13255.4 15183.2 1.14544
166 gamma-soluble nsf attachment protein (snap-gamma) (n-ethylmaleimide- sensitive factor attachment protein, gamma). [swissprot;acc:q99747] 1 209.299 249.187 1.19058
my016 protein. [sptrembl;acc:q9h3k6] 0 5561.19 6366.91 1.14488
167 glutamate decarboxylase, 67 kda isoform (ec 4.1.1.15) (gad-67) (67 kda glutamic acid decarboxylase). [swissprot;acc:q99259] 1 209.299 249.187 1.19058
signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 0 12157.6 13890.3 1.14252
168 fos-related antigen 2. [swissprot;acc:p15408] 7091.75 6217.28 1.14065
gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 1 82.5916 98.0548 1.18722
169 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 0 9875.43 11256.8 1.13988
apg3p; pc3-96 protein. [refseq;acc:nm_022488] 1 82.5916 98.0548 1.18722
170 low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] 0 11364 12941 1.13877
nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 1 227.199 192.715 1.17894
171 lamin b2. [swissprot;acc:q03252] 0 12135.4 13802 1.13733
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 1 227.202 192.823 1.17829
172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] 174.667 205.556 1.17685
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] 0 12225.7 13893.1 1.13638
173 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 1 227.032 193.056 1.17599
suppressor of actin 1. [refseq;acc:nm_014016] 0 19088.1 16804.6 1.13589
174 dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] 1 335 286 1.17133
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] 0 13248.5 11666.4 1.13561
175 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] 1 199.949 234.187 1.17123
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] 0 13248.5 11666.4 1.13561
176 dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] 13068 11528 1.13359
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 1 275.754 235.908 1.1689
177 dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] 229.406 196.695 1.1663
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 0 14922.7 13174.5 1.1327
178 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 1 226.887 194.72 1.1652
integral membrane protein cii-3b. [sptrembl;acc:o75609] 0 14951.6 13204.2 1.13234
179 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 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
180 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] 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
182 histone acetyltransferase type b catalytic subunit (ec 2.3.1.48). [swissprot;acc:o14929] 1 277.546 240.461 1.15422
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 0 11573.8 10231.3 1.13121
183 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 1 228.306 198.011 1.153
ubiquitin activating enzyme e1-like protein. [refseq;acc:nm_006395] 0 11613 13133.5 1.13093
184 odd-skipped related 1; odz (odd oz/ten-m) related 1. [refseq;acc:nm_145260] 1 274.027 237.79 1.15239

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/