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 1313 to 1362 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
657 anaphase-promoting complex subunit 2; anaphase-promoting complex 2. [refseq;acc:nm_013366] Subtracted 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
667 coatomer beta' subunit (beta'-coat protein) (beta'-cop) (p102). [swissprot;acc:p35606] Subtracted 10075.5 9377.75 697.75
tubby related protein 1 (tubby-like protein 1). [swissprot;acc:o00294] Divided 6374.65 7145.59 1.12094
668 coatomer gamma subunit (gamma-coat protein) (gamma-cop). [swissprot;acc:q9y678] Subtracted 10075.5 9377.75 697.75
vacuolar protein sorting 29 (vesicle protein sorting 29) (hvps29) (mds007) (pep11) (dc7/dc15). [swissprot;acc:q9ubq0] Divided 6374.65 7145.59 1.12094
669 coatomer zeta-1 subunit (zeta-1 coat protein) (zeta-1 cop) (cgi-120) (hspc181). [swissprot;acc:q9y3c3] Subtracted 10075.5 9377.75 697.75
numb-like protein (numb-r). [swissprot;acc:q9y6r0] Divided 6374.65 7145.59 1.12094
670 coatomer delta subunit (delta-coat protein) (delta-cop) (archain). [swissprot;acc:p48444] Subtracted 10075.5 9377.75 697.75
tubby related protein 3 (tubby-like protein 3). [swissprot;acc:o75386] Divided 6374.65 7145.59 1.12094
671 peptidyl-prolyl cis-trans isomerase e (ec 5.2.1.8) (ppiase e) (rotamase e) (cyclophilin e) (cyclophilin 33). [swissprot;acc:q9unp9] Subtracted 10075.5 9377.75 697.75
vacuolar protein sorting 35 (vesicle protein sorting 35) (hvps35) (maternal-embryonic 3). [swissprot;acc:q96qk1] Divided 6374.65 7145.59 1.12094
672 coatomer zeta-2 subunit (zeta-2 coat protein) (zeta-2 cop). [swissprot;acc:q9p299] Subtracted 10075.5 9377.75 697.75
protein kinase c, zeta type (ec 2.7.1.37) (npkc-zeta). [swissprot;acc:q05513] Divided 6374.65 7145.59 1.12094
673 fibulin-1 precursor. [swissprot;acc:p23142] Subtracted 8550.79 9248.06 697.27
transcription factor btf3 (rna polymerase b transcription factor 3). [swissprot;acc:p20290] Divided 6933.17 7766.54 1.1202
674 hcv ns3-transactivated protein 1. [refseq;acc:nm_019048] Subtracted 6000.23 6696.89 696.66
sprouty homolog 4 (spry-4). [swissprot;acc:q9c004] Divided 5549.2 6215.42 1.12006
675 sprouty homolog 3 (spry-3). [swissprot;acc:o43610]
vacuolar atp synthase catalytic subunit a, ubiquitous isoform (ec 3.6.3.14) (v-atpase a subunit 1) (vacuolar proton pump alpha subunit 1) (v-atpase 69 kda subunit 1) (isoform va68). [swissprot;acc:p38606] Subtracted 6000.23 6696.89 696.66
676 asparagine synthetase [glutamine-hydrolyzing] (ec 6.3.5.4) (glutamine- dependent asparagine synthetase) (ts11 cell cycle control protein). [swissprot;acc:p08243]
sprouty homolog 1 (spry-1) (fragment). [swissprot;acc:o43609] Divided 5549.2 6215.42 1.12006
677 dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] Subtracted 4024.4 4719.35 694.95
sprouty homolog 2 (spry-2). [swissprot;acc:o43597] Divided 5549.2 6215.42 1.12006
678 cytoplasmic protein nck1 (nck adaptor protein 1) (sh2/sh3 adaptor protein nck-alpha). [swissprot;acc:p16333] Subtracted 6784.67 7475.48 690.81
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Divided 6938.22 7770.65 1.11998
679 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] 6503.1 7282.94 1.11992
n-acetylgalactosamine kinase (ec 2.7.1.-) (galnac kinase) (galactokinase 2). [swissprot;acc:q01415] Subtracted 4910.6 5600.61 690.01
680 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Divided 6503.03 7282.5 1.11986
galactose-1-phosphate uridylyltransferase (ec 2.7.7.12) (gal-1-p uridylyltransferase) (udp-glucose--hexose-1-phosphate uridylyltransferase). [swissprot;acc:p07902] Subtracted 4910.6 5600.61 690.01
681 ribosomal protein l24-like; 60s ribosomal protein l30 isolog; my024 protein; homolog of yeast ribosomal like protein 24. [refseq;acc:nm_016304] Divided 7170.83 8029.64 1.11976
udp-glucose 4-epimerase (ec 5.1.3.2) (galactowaldenase) (udp- galactose 4-epimerase). [swissprot;acc:q14376] Subtracted 4910.6 5600.61 690.01

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/