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 1283 to 1332 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
642 atpase inhibitor, mitochondrial precursor. [swissprot;acc:q9uii2] Divided 4810.85 5414.23 1.12542
elongation of very long chain fatty acids protein 1 (cgi-88). [swissprot;acc:q9bw60] Subtracted 4890.55 5610.96 720.41
643 polyamine oxidase isoform 1; polyamine oxidase; flavin-containing spermine oxidase; putative cyclin g1 interacting protein; flavin containing amine oxidase. [refseq;acc:nm_019025] Divided 4810.85 5414.23 1.12542
scratch; scratch 1. [refseq;acc:nm_031309] Subtracted 7281.6 8001.64 720.04
644 cytochrome c-type heme lyase (ec 4.4.1.17) (cchl) (holocytochrome c- type synthase). [swissprot;acc:p53701] Divided 4810.85 5414.22 1.12542
proteasome subunit alpha type 5 (ec 3.4.25.1) (proteasome zeta chain) (macropain zeta chain) (multicatalytic endopeptidase complex zeta chain). [swissprot;acc:p28066] Subtracted 5713.41 6432.92 719.51
645 glutathione s-transferase theta 1 (ec 2.5.1.18) (gst class-theta) (glutathione transferase t1-1). [swissprot;acc:p30711] Divided 4810.71 5413.89 1.12538
myc proto-oncogene protein (c-myc). [swissprot;acc:p01106] Subtracted 4892.16 5611.48 719.32
646 dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] 7273.78 7991.72 717.94
fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] Divided 4019.88 4522.61 1.12506
647 potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Subtracted 2411.93 1695.45 716.48
short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] Divided 5167.88 4594.43 1.12481
648 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Subtracted 2414.22 1698.12 716.1
splicing factor 3a subunit 3 (spliceosome associated protein 61) (sap 61) (sf3a60). [swissprot;acc:q12874] Divided 5248.07 5901.72 1.12455
649 potassium voltage-gated channel, shal-related subfamily, member 3 isoform 1; sha1-related potassium channel kv4.3; voltage-gated k+ channel; potassium ionic channel kv4.3; voltage-gated potassium channel kv4.3. [refseq;acc:nm_004980] Subtracted 2414.77 1698.75 716.02
splicing factor 3 subunit 1 (spliceosome associated protein 114) (sap 114) (sf3a120). [swissprot;acc:q15459] Divided 5248.07 5901.72 1.12455
650 golgi reassembly stacking protein 2; golgi reassembly stacking protein 2, 55 kda. [refseq;acc:nm_015530] 8362.81 9402.7 1.12435
potassium voltage-gated channel, shal-related subfamily, member 1; shal-type potassium channel; voltage-gated potassium channel kv4.1. [refseq;acc:nm_004979] Subtracted 2416.53 1700.8 715.73
651 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] Divided 5168.43 4597.44 1.1242
n-terminal acetyltransferase complex ard1 subunit homolog (ec 2.3.1.-). [swissprot;acc:p41227] Subtracted 4509.54 5223.95 714.41
652 importin alpha-3 subunit (karyopherin alpha-3 subunit) (srp1-gamma). [swissprot;acc:o00505] 6456.35 7169.75 713.4
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Divided 5168.43 4597.44 1.1242
653 dna topoisomerase ii, alpha isozyme (ec 5.99.1.3). [swissprot;acc:p11388] Subtracted 6441.17 7154.55 713.38
methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] Divided 5560.06 6248.27 1.12378
654 histone h3.3 (h3.a) (h3.b) (h3.3q). [swissprot;acc:p06351] 4088.63 4593.43 1.12346
target of egr1, member 1 (nuclear); target of egr1, member 1. [refseq;acc:nm_025077] Subtracted 6455.66 7168.82 713.16
655 dj1099d15.1 (putative dnaj protein). [sptrembl;acc:q9h4j9] Divided 4088.63 4593.43 1.12346
dna topoisomerase ii, beta isozyme (ec 5.99.1.3). [swissprot;acc:q02880] Subtracted 6441.14 7154.13 712.99
656 apolipoprotein a-i binding protein; apoa-i binding protein. [refseq;acc:nm_144772] Divided 6139.04 6893.7 1.12293
importin alpha-4 subunit (karyopherin alpha-4 subunit) (qip1 protein). [swissprot;acc:o00629] Subtracted 6455.02 7167.96 712.94
657 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] 10341.2 9630.35 710.85
rgs19-interacting protein 1 (gaip c-terminus interacting protein gipc) (rgs-gaip interacting protein) (tax interaction protein 2) (tip-2). [swissprot;acc:o14908] Divided 6079.26 6824.47 1.12258
658 apical-like protein (apxl protein). [swissprot;acc:q13796] 6088.77 6834.87 1.12254
bag-family molecular chaperone regulator-3 (bcl-2 binding athanogene- 3) (bag-3) (bcl-2-binding protein bis) (docking protein cair-1). [swissprot;acc:o95817] Subtracted 4522.71 5233.14 710.43
659 histone acetyltransferase type b subunit 2 (retinoblastoma binding protein p46) (retinoblastoma-binding protein 7) (rbbp-7). [swissprot;acc:q16576] 4858.96 5568.85 709.89
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Divided 6089.21 6835.34 1.12253
660 metastasis-associated protein mta1. [swissprot;acc:q13330] Subtracted 4864.25 5573.62 709.37
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Divided 5575.18 6254.85 1.12191
661 chromatin assembly factor 1 subunit c (caf-1 subunit c) (chromatin assembly factor i p48 subunit) (caf-i 48 kda subunit) (caf-ip48) (retinoblastoma binding protein p48) (retinoblastoma-binding protein 4) (rbbp-4) (msi1 protein homolog). [swissprot;acc:q09028] Subtracted 4869.15 5578.02 708.87
step ii splicing factor slu7. [refseq;acc:nm_006425] Divided 5575.18 6254.85 1.12191
662 cytoplasmic protein nck2 (nck adaptor protein 2) (sh2/sh3 adaptor protein nck-beta) (nck-2). [swissprot;acc:o43639] Subtracted 6776.85 7485.55 708.7
partitioning defective-6 homolog gamma (par-6 gamma) (par6d). [swissprot;acc:q9byg4] Divided 6374.65 7145.59 1.12094
663 isocitrate dehydrogenase [nadp], mitochondrial precursor (ec 1.1.1.42) (oxalosuccinate decarboxylase) (idh) (nadp+-specific icdh) (idp) (icd-m). [swissprot;acc:p48735] Subtracted 7937.72 8646.38 708.66
tubby protein homolog. [swissprot;acc:p50607] Divided 6374.65 7145.59 1.12094
664 pms1 protein homolog 2 (dna mismatch repair protein pms2). [swissprot;acc:p54278] Subtracted 6231.31 6933.9 702.59
protein kinase c, iota type (ec 2.7.1.37) (npkc-iota) (atypical protein kinase c-lamda/iota) (apkc-lambda/iota). [swissprot;acc:p41743] Divided 6374.65 7145.59 1.12094
665 lupus la protein (sjogren syndrome type b antigen) (ss-b) (la ribonucleoprotein) (la autoantigen). [swissprot;acc:p05455] Subtracted 4108.15 4808.93 700.78
numb protein homolog (h-numb) (protein s171). [swissprot;acc:p49757] Divided 6374.65 7145.59 1.12094
666 epididymal secretory protein e1 precursor (niemann-pick disease type c2 protein) (epi-1) (he1) (epididymal secretory protein 14.6) (esp14.6). [swissprot;acc:q15668] Subtracted 6781.05 7480.15 699.1
tbc1 domain family member 5. [swissprot;acc:q92609] Divided 6374.65 7145.59 1.12094

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/