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 1344 to 1393 of 6456 in total
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
red
green
network_comparison
672 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
682 methionyl-trna synthetase (ec 6.1.1.10) (methionine--trna ligase) (metrs). [swissprot;acc:p56192] 5560.06 6248.27 688.21
syntaxin 12. [refseq;acc:nm_177424] Divided 5552.92 6217.59 1.1197
683 dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Subtracted 3751.3 4431.34 680.04
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Divided 7139.5 7994.06 1.11969
684 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 4359.82 4880.99 1.11954
u2 small nuclear ribonucleoprotein auxiliary factor 35 kda subunit related-protein 1. [swissprot;acc:q15695] Subtracted 5575.18 6254.85 679.67
685 metaxin 1. [swissprot;acc:q13505] Divided 9327.58 10442.2 1.1195
step ii splicing factor slu7. [refseq;acc:nm_006425] Subtracted 5575.18 6254.85 679.67
686 5'-amp-activated protein kinase, gamma-1 subunit (ampk gamma-1 chain) (ampkg). [swissprot;acc:p54619] Divided 6920.69 7747.63 1.11949
uba/ubx 33.3 kda protein. [swissprot;acc:q04323] Subtracted 6562.98 7242.37 679.39
687 5'-amp-activated protein kinase, catalytic alpha-2 chain (ec 2.7.1.-) (ampk alpha-2 chain). [swissprot;acc:p54646] Divided 6920.71 7747.65 1.11949
ero1-like. [refseq;acc:nm_014584] Subtracted 6562.98 7242.37 679.39
688 5'-amp-activated protein kinase, catalytic alpha-1 chain (ec 2.7.1.-) (ampk alpha-1 chain). [swissprot;acc:q13131] Divided 6920.67 7747.6 1.11949
retinoblastoma-like protein 1 (107 kda retinoblastoma-associated protein) (prb1) (p107). [swissprot;acc:p28749] Subtracted 6311.83 6989.6 677.77
689 5'-amp-activated protein kinase, beta-2 subunit (ampk beta-2 chain). [swissprot;acc:o43741] Divided 6920.69 7747.63 1.11949
retinoblastoma-like protein 2 (130 kda retinoblastoma-associated protein) (prb2) (p130) (rbr-2). [swissprot;acc:q08999] Subtracted 6311.6 6989.33 677.73
690 5'-amp-activated protein kinase, gamma-3 subunit (ampk gamma-3 chain) (ampk gamma3). [swissprot;acc:q9ugi9] Divided 6920.69 7747.63 1.11949
trna isopentenylpyrophosphate transferase. [refseq;acc:nm_017646] Subtracted 6257.99 6932.95 674.96
691 5'-amp-activated protein kinase, beta-1 subunit (ampk beta-1 chain) (ampkb). [swissprot;acc:q9y478] Divided 6920.69 7747.63 1.11949
t-complex protein 1, epsilon subunit (tcp-1-epsilon) (cct-epsilon). [swissprot;acc:p48643] Subtracted 8425.35 7751.57 673.78
692 5'-amp-activated protein kinase, gamma-2 subunit (ampk gamma-2 chain) (ampk gamma2) (h91620p). [swissprot;acc:q9ugj0] Divided 6920.69 7747.63 1.11949
e-1 enzyme. [refseq;acc:nm_021204] Subtracted 6603.09 7274.72 671.63
693 eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] 3199.4 3870.8 671.4
j kappa-recombination signal binding protein (rbp-j kappa). [swissprot;acc:q06330] Divided 7725.1 8647.74 1.11943
694 human immunodeficiency virus type i enhancer binding protein 3. [refseq;acc:nm_024503]
orphan nuclear receptor nr6a1 (germ cell nuclear factor) (gcnf) (retinoid receptor-related testis specific receptor) (rtr). [swissprot;acc:q15406] Subtracted 6075.55 6746.92 671.37
695 vacuolar atp synthase 16 kda proteolipid subunit (ec 3.6.3.14). [swissprot;acc:p27449] 5768.32 6434.78 666.46
zinc finger protein 40 (human immunodeficiency virus type i enhancer- binding protein 1) (hiv-ep1) (major histocompatibility complex binding protein 1) (mbp-1) (positive regulatory domain ii binding factor 1) (prdii-bf1). [swissprot;acc:p15822] Divided 7725.1 8647.74 1.11943
696 human immunodeficiency virus type i enhancer-binding protein 2 (hiv-ep2). [swissprot;acc:p31629]
sarcoglycan zeta; zeta-sarcoglycan. [refseq;acc:nm_139167] Subtracted 5768.32 6434.78 666.46
697 golgi complex associated protein 1; golgi resident protein gcp60; peripherial benzodiazepine receptor associated protein; golgi phosphoprotein 1; pbr associated protein; pka (rialpha)-associated protein. [refseq;acc:nm_022735]

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/