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 675 to 724 of 7460 in total
Value Type  : Ranked
Interaction Map  : High confidence
Rank
description
Network Comparison Type
Filtered
red
green
network_comparison
169 cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] Subtracted 1 312 284 28
pp3111 protein. [refseq;acc:nm_022156] 0 6185 7603 1418
170 huntingtin interacting protein c. [refseq;acc:nm_012272] 1 227.971 200.417 27.554
low affinity immunoglobulin epsilon fc receptor (lymphocyte ige receptor) (fc-epsilon-rii) (cd23) (blast-2) (immunoglobulin e-binding factor). [swissprot;acc:p06734] Divided 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
t-complex protein 1, zeta subunit (tcp-1-zeta) (cct-zeta) (cct-zeta-1) (tcp20) (htr3). [swissprot;acc:p40227] Subtracted 0 12715.9 11333.2 1382.7
171 alanine aminotransferase (ec 2.6.1.2) (glutamic--pyruvic transaminase) (gpt) (glutamic--alanine transaminase). [swissprot;acc:p24298] 9875.43 11256.8 1381.37
lamin b2. [swissprot;acc:q03252] Divided 12135.4 13802 1.13733
nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 1 227.202 192.823 1.17829
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Subtracted 201.478 228.784 27.306
172 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 0 15260.6 13895.8 1364.8
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Divided 1 174.667 205.556 1.17685
ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Subtracted 201.515 228.752 27.237
zinc finger protein slug (neural crest transcription factor slug) (snail homolog 2). [swissprot;acc:o43623] Divided 0 12225.7 13893.1 1.13638
173 nucleoporin nup43 (p42). [swissprot;acc:q8nfh3] Subtracted 4338.65 5700.79 1362.14
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 1 201.515 228.752 27.237
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 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
kappa b-ras 1. [refseq;acc:nm_020345] Subtracted 0 12657.7 11299.1 1358.6
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 1 228.1 200.968 27.132
ribulose-5-phosphate-3-epimerase; ribulose 5-phosphate 3-epimerase. [refseq;acc:nm_006916] Divided 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
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Subtracted 228.085 201.006 27.079
putative inorganic polyphosphate/atp-nad kinase (ec 2.7.1.23) (poly(p)/atp nad kinase). [swissprot;acc:o95544] 0 11573.8 10231.3 1342.5
thiamin pyrophosphokinase 1; mouse thiamin pyrophosphokinase homolog; thiamine pyrophosphokinase. [refseq;acc:nm_022445] Divided 13248.5 11666.4 1.13561
176 40s ribosomal protein s2 (s4) (llrep3 protein). [swissprot;acc:p15880] Subtracted 11935.1 10592.8 1342.3
dead-box protein abstrakt homolog. [swissprot;acc:q9ujv9] Divided 13068 11528 1.13359
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] 1 275.754 235.908 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
pnas-18. [sptrembl;acc:q9bzu3] Subtracted 0 12602.7 13939.6 1336.9
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 14922.7 13174.5 1.1327
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

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/