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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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 red Value Type green Rank Interaction Map description Filtered network_comparison
Results: HTML CSV LaTeX Showing element 727 to 776 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
red
green
Rank
description
network_comparison
3936.2 3755.33 2220 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 1.04816
3936.33 3755.5 2221 thrombospondin 3 precursor. [swissprot;acc:p49746] 1.04815
3946.32 4475.47 592 histone h2b.c (h2b/c). [swissprot;acc:q99880] 1.13409
593 histone h2b.q (h2b/q) (h2b-gl105). [swissprot;acc:q16778]
594 histone h3.1 (h3/a) (h3/c) (h3/d) (h3/f) (h3/h) (h3/i) (h3/j) (h3/k) (h3/l). [swissprot;acc:p16106]
595 histone h2b. [refseq;acc:nm_175055]
596 histone h2b.s (h2b/s). [swissprot;acc:p57053]
597 histone h2b.d (h2b/d). [swissprot;acc:q99877]
598 histone h3.4 (h3t) (h3/t) (h3/g). [swissprot;acc:q16695]
599 testis-specific histone h2b; h2b histone family, member u, (testis-specific). [refseq;acc:nm_170610]
600 histone h2b.e (h2b/e). [swissprot;acc:q99879]
3953.53 3972.32 2685 cytochrome c1, heme protein, mitochondrial precursor (cytochrome c-1). [swissprot;acc:p08574] 1.00475
2686 oligophrenin-1 like protein (gtpase regulator associated with focal adhesion kinase). [swissprot;acc:q9una1]
2687 senescence marker protein-30 (smp-30) (regucalcin) (rc). [swissprot;acc:q15493]
2688 oligophrenin 1. [swissprot;acc:o60890]
3956.25 4364.25 871 protein bap28. [swissprot;acc:q9h583] 1.10313
3964.71 4042.75 2564 t-cell leukemia homeobox protein 3 (homeobox protein hox-11l2). [swissprot;acc:o43711] 1.01968
2565 homeobox protein barh-like 1. [swissprot;acc:q9hbu1]
2566 opsin 4 (melanopsin). [swissprot;acc:q9uhm6]
2567 t-cell leukemia homeobox protein 2 (homeobox protein hox-11l1) (neural crest homeobox protein). [swissprot;acc:o43763]
2568 t-cell leukemia homeobox protein 1 (homeobox protein hox-11) (tcl-3 proto-oncogene). [swissprot;acc:p31314]
2569 hect domain containing protein 1 (fragment). [swissprot;acc:q9ult8]
2570 homeobox protein barh-like 2. [swissprot;acc:q9umq3]
3975.77 4485.05 612 eukaryotic translation initiation factor 3 subunit 2 (eif-3 beta) (eif3 p36) (eif3i) (tgf-beta receptor interacting protein 1) (trip-1). [swissprot;acc:q13347] 1.1281
613 trinucleotide repeat containing 15. [refseq;acc:nm_015575]
3976.48 3816.38 2376 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 1.04195
3976.92 3804.85 2308 60s ribosomal protein l7. [swissprot;acc:p18124] 1.04522
3977.7 3818.01 2377 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 1.04183
3977.76 3818.09 2378 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 1.04182
3979.06 3819.84 2379 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 1.04168
3985.17 3928.38 2630 polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 1.01446
3996.81 4465.61 713 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] 1.11729
4000.73 3947.54 2633 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 1.01347
4019.88 4522.61 646 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 1.12506
4024.4 4719.35 367 dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 1.17268
4025.3 4474.3 791 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] 1.11154
4031.94 4166.99 2446 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 1.0335
4039.81 4484.22 809 wd-repeat protein 3. [swissprot;acc:q9unx4] 1.11001
4049 4477.43 836 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] 1.10581
4052.77 4612.54 546 zinc finger protein t86. [swissprot;acc:o00488] 1.13812
4057.54 4457.66 923 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 1.09861
4062.03 4492.48 831 t-cell activation wd repeat protein. [refseq;acc:nm_139281] 1.10597
4063.64 4492.98 837 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 1.10565
4064.23 4493.36 838 pbk1 protein. [sptrembl;acc:o76021] 1.10559
4066.56 4491.65 848 wd-repeat protein bing4. [swissprot;acc:o15213] 1.10453
4068.56 5252.6 181 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 1.29102
4068.78 5082.18 208 voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 1.24907
209 voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359]
4068.82 5082.21 210 voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 1.24906
4068.91 5082.27 211 voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 1.24905

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/