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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Gene Network Comparison Type red Value Type green Rank Interaction Map description Filtered network_comparison
Results: HTML CSV LaTeX Showing element 808 to 857 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
red
green
Rank
description
network_comparison
4133.47 5945.32 80 nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 1.43834
4134.77 4691.24 568 grpe protein homolog 2, mitochondrial precursor (mt-grpe#2). [swissprot;acc:q8taa5] 1.13458
569 grpe protein homolog 1, mitochondrial precursor (mt-grpe#1) (hmge). [swissprot;acc:q9hav7]
570 swi/snf-related matrix-associated actin-dependent regulator of chromatin d2; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60b; swp73-like protein; chromatin remodeling complex baf60b subunit; swi/snf complex 60 kda subunit b. [refseq;acc:nm_003077]
571 swi/snf-related matrix-associated actin-dependent regulator of chromatin d3; rsc6p; mammalian chromatin remodeling complex brg1-associated factor 60c; swp73-like protein; chromatin remodeling complex baf60c subunit; swi/snf complex 60 kda subunit c. [refseq;acc:nm_003078]
572 swi/snf related, matrix associated, actin dependent regulator of chromatin subfamily d member 1 (swi/snf complex 60 kda subunit) (brg1- associated factor 60a). [swissprot;acc:q96gm5]
4136.36 5943.56 81 nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 1.43691
4137.61 4152.72 2705 protein cgi-27 (c21orf19-like protein). [swissprot;acc:q9y316] 1.00365
4163.36 4145.95 2698 trub pseudouridine (psi) synthase homolog 1. [refseq;acc:nm_139169] 1.0042
4164.76 4337.01 2383 calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 1.04136
4164.96 4336.92 2384 calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 1.04129
4172.91 5954.48 82 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 1.42694
4180.32 4253.46 2584 deformed epidermal autoregulatory factor 1 homolog (nuclear deaf-1 related transcriptional regulator) (nudr) (suppressin) (zinc finger mynd domain containing protein 5). [swissprot;acc:o75398] 1.0175
2585 rio kinase 1 isoform 1; ad034 protein. [refseq;acc:nm_031480]
2586 map/microtubule affinity-regulating kinase 1. [refseq;acc:nm_018650]
2587 map/microtubule affinity-regulating kinase 2 isoform b; elkl motif kinase 1; elkl motif kinase. [refseq;acc:nm_004954]
2588 meiotic recombination protein spo11. [swissprot;acc:q9y5k1]
4188.5 4194.22 2746 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 1.00137
4191.15 4226.86 2656 zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] 1.00852
4200.59 4210.94 2740 dna-directed rna polymerases i, ii, and iii 17.1 kda polypeptide (ec 2.7.7.6) (rpb17) (rpb8) (rpabc3). [swissprot;acc:p52434] 1.00246
4241.57 5810.79 104 musashi 2 isoform a. [refseq;acc:nm_138962] 1.36996
105 musashi 1. [refseq;acc:nm_002442]
106 nuclear protein ukp68. [refseq;acc:nm_024824]
4243.44 4352.56 2507 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 1.02571
4244.95 5193.42 260 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1.22343
4245.52 5942.75 93 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 1.39977
4246.95 5208.98 243 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 1.22652
4247.36 5192.61 261 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1.22255
4247.86 5941.88 94 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 1.39879
4250.14 5211.25 244 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 1.22614
4250.18 4729.12 764 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 1.11269
4250.54 4729.67 763 6-phosphofructokinase, muscle type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme a) (pfk-a) (phosphofructokinase-m). [swissprot;acc:p08237] 1.11272
4251.65 5212.33 245 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 1.22595
4252.66 5213.05 246 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 1.22583
4254.62 4736.03 759 6-phosphofructokinase, type c (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme c) (pfk-c) (6-phosphofructokinase, platelet type). [swissprot;acc:q01813] 1.11315
4266.04 5843.51 107 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 1.36977
4280.99 4697.02 950 bystin. [swissprot;acc:q13895] 1.09718
4300.46 4334.66 2662 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 1.00795
4300.47 5807.72 114 huntingtin interacting protein c. [refseq;acc:nm_012272] 1.35048
4307.12 4755.03 851 casein kinase ii, alpha chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19138] 1.10399
852 casein kinase ii, alpha' chain (ck ii) (ec 2.7.1.37). [swissprot;acc:p19784]
4322.65 4696.04 1203 geranylgeranyl pyrophosphate synthetase (ggpp synthetase) (ggppsase) (geranylgeranyl diphosphate synthase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10); farnesyltranstransferase (ec 2.5.1.29)]. [swissprot;acc:o95749] 1.08638
4327.94 4248.77 2574 katanin p60 subunit a 1. [refseq;acc:nm_007044] 1.01863
4331.17 4771.22 894 parafibromin. [refseq;acc:nm_024529] 1.1016
4331.35 4700.91 1224 splicing factor 3b subunit 4 (spliceosome associated protein 49) (sap 49) (sf3b50) (pre-mrna splicing factor sf3b 49 kda subunit). [swissprot;acc:q15427] 1.08532
4331.39 4252.8 2580 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] 1.01848
4336.58 4310.3 2669 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 1.0061
4336.62 4310.35 2670 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 1.00609
4338.49 4725.86 1121 nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] 1.08929
4338.79 4313.52 2671 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 1.00586

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/