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 - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Network Comparison Type Value Type red Rank green Interaction Map description Filtered network_comparison
Results: HTML CSV LaTeX Showing element 818 to 867 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
red
Rank
green
description
network_comparison
4164.96 2384 4336.92 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 82 5954.48 small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] 1.42694
4180.32 2584 4253.46 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 2746 4194.22 hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 1.00137
4191.15 2656 4226.86 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 2740 4210.94 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
4241.57 104 5810.79 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 2507 4352.56 mevalonate kinase (ec 2.7.1.36) (mk). [swissprot;acc:q03426] 1.02571
4244.95 260 5193.42 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1.22343
4245.52 93 5942.75 formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] 1.39977
4246.95 243 5208.98 homer, neuronal immediate early gene, 2; homer homolog 3 (drosophila). [refseq;acc:nm_004839] 1.22652
4247.36 261 5192.61 signal recognition particle 9 kda protein (srp9). [swissprot;acc:p49458] 1.22255
4247.86 94 5941.88 huntingtin-interacting protein hypa/fbp11 (fragment). [sptrembl;acc:o75404] 1.39879
4250.14 244 5211.25 ubiquinone biosynthesis protein coq7 homolog (coenzyme q biosynthesis protein 7 homolog) (timing protein clk-1 homolog). [swissprot;acc:q99807] 1.22614
4250.18 764 4729.12 6-phosphofructokinase, liver type (ec 2.7.1.11) (phosphofructokinase 1) (phosphohexokinase) (phosphofructo-1-kinase isozyme b) (pfk-b). [swissprot;acc:p17858] 1.11269
4250.54 763 4729.67 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
4251.65 245 5212.33 homer, neuronal immediate early gene, 1b. [refseq;acc:nm_004272] 1.22595
4252.66 246 5213.05 homer, neuronal immediate early gene, 3. [refseq;acc:nm_004838] 1.22583
4254.62 759 4736.03 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
4266.04 107 5843.51 20 kda nuclear cap binding protein (ncbp 20 kda subunit) (cbp20) (ncbp interacting protein 1) (nip1). [swissprot;acc:p52298] 1.36977
4280.99 950 4697.02 bystin. [swissprot;acc:q13895] 1.09718
4300.46 2662 4334.66 dj408b20.3 (novel protein similar to 60s acidic ribosomal protein p2 (rplp2)). [sptrembl;acc:q9h5a9] 1.00795
4300.47 114 5807.72 huntingtin interacting protein c. [refseq;acc:nm_012272] 1.35048
4307.12 851 4755.03 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 1203 4696.04 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 2574 4248.77 katanin p60 subunit a 1. [refseq;acc:nm_007044] 1.01863
4331.17 894 4771.22 parafibromin. [refseq;acc:nm_024529] 1.1016
4331.35 1224 4700.91 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 2580 4252.8 katanin p80 subunit b 1; katanin (80 kda); katanin p80 (wd40-containing) subunit b 1. [refseq;acc:nm_005886] 1.01848
4336.58 2669 4310.3 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 1.0061
4336.62 2670 4310.35 dipeptidylpeptidase 9; dipeptidyl peptidase 9; dipeptidyl peptidase iv-related protein-2. [refseq;acc:nm_139159] 1.00609
4338.49 1121 4725.86 nucleolar protein nop5 (nucleolar protein 5) (nop58) (hspc120). [swissprot;acc:q9y2x3] 1.08929
4338.79 2671 4313.52 muscle-specific beta 1 integrin binding protein. [refseq;acc:nm_014446] 1.00586
4355.61 128 5810.82 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 1.3341
4358.13 129 5811.49 luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 1.33348
4359.82 684 4880.99 eukaryotic translation initiation factor 3 subunit 9 (eif-3 eta) (eif3 p116) (eif3 p110) (eif3b). [swissprot;acc:p55884] 1.11954
4366.44 108 5899.76 filamin b, beta (actin binding protein 278); beta filamin; filamin 1 (actin-binding protein-280)-like; filamin b, beta (actin-binding protein-278); filamin b, beta. [refseq;acc:nm_001457] 1.35116
109 rev1-like; rev1 protein; rev1 (yeast homolog)- like. [refseq;acc:nm_016316]
110 protein arginine n-methyltransferase 1 (ec 2.1.1.-) (interferon receptor 1-bound protein 4). [swissprot;acc:q99873]
111 protein arginine n-methyltransferase 4 (ec 2.1.1.-). [swissprot;acc:q9nr22]
112 u1 small nuclear ribonucleoprotein 70 kda (u1 snrnp 70 kda) (snrnp70) (u1-70k). [swissprot;acc:p08621]
113 filamin a (alpha-filamin) (filamin 1) (endothelial actin-binding protein) (abp-280) (nonmuscle filamin). [swissprot;acc:p21333]
4367.69 2599 4438.77 alanyl-trna synthetase (ec 6.1.1.7) (alanine--trna ligase) (alars). [swissprot;acc:p49588] 1.01627

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/