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 red Value Type Rank green Interaction Map description Filtered network_comparison
Results: HTML CSV LaTeX Showing element 725 to 774 of 3228 in total
Network Comparison Type  : Divided
Value Type  : Measured
Interaction Map  : High confidence
Filtered  : 1
red
Rank
green
description
network_comparison
3926.4 2583 3857.88 polymerase (rna) iii (dna directed) (32kd). [refseq;acc:nm_006467] 1.01776
3933.74 2628 3877.14 40s ribosomal protein s9. [swissprot;acc:p46781] 1.0146
3936.2 2220 3755.33 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 1.04816
3936.33 2221 3755.5 thrombospondin 3 precursor. [swissprot;acc:p49746] 1.04815
3946.32 592 4475.47 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 2685 3972.32 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]
3956.25 871 4364.25 protein bap28. [swissprot;acc:q9h583] 1.10313
3964.71 2564 4042.75 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]
3975.77 612 4485.05 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 2376 3816.38 cysteine-rich protein 1 (crp1) (crp). [swissprot;acc:p21291] 1.04195
3976.92 2308 3804.85 60s ribosomal protein l7. [swissprot;acc:p18124] 1.04522
3977.7 2377 3818.01 likely ortholog of mouse shc sh2-domain binding protein 1. [refseq;acc:nm_024745] 1.04183
3977.76 2378 3818.09 smooth muscle cell lim protein (cysteine-rich protein 2) (crp2) (lim-only protein 5). [swissprot;acc:q16527] 1.04182
3979.06 2379 3819.84 lim domain protein, cardiac (muscle lim protein) (cysteine-rich protein 3) (crp3). [swissprot;acc:p50461] 1.04168
3985.17 2630 3928.38 polymerase (rna) iii (dna directed) (62kd). [refseq;acc:nm_006468] 1.01446
3996.81 713 4465.61 upf0202 protein kiaa1709. [swissprot;acc:q9h0a0] 1.11729
4000.73 2633 3947.54 dna-directed rna polymerases iii 39 kda polypeptide (ec 2.7.7.6) (rna polymerase iii c39 subunit). [swissprot;acc:q9h1d9] 1.01347
4019.88 646 4522.61 fibrillarin (34 kda nucleolar scleroderma antigen). [swissprot;acc:p22087] 1.12506
4024.4 367 4719.35 dna polymerase epsilon, catalytic subunit a (ec 2.7.7.7) (dna polymerase ii subunit a). [swissprot;acc:q07864] 1.17268
4025.3 791 4474.3 transducin beta-like 3; wd-repeat protein sazd. [refseq;acc:nm_006453] 1.11154
4031.94 2446 4166.99 dna-directed rna polymerase ii 16 kda polypeptide (ec 2.7.7.6) (rpb4). [swissprot;acc:o15514] 1.0335
4039.81 809 4484.22 wd-repeat protein 3. [swissprot;acc:q9unx4] 1.11001
4049 836 4477.43 atp-dependent rna helicase rok1; atp-dependent rna helicase. [refseq;acc:nm_007010] 1.10581
4052.77 546 4612.54 zinc finger protein t86. [swissprot;acc:o00488] 1.13812
4057.54 923 4457.66 eukaryotic translation initiation factor 3 subunit 8 (eif3 p110) (eif3c). [swissprot;acc:q99613] 1.09861
4062.03 831 4492.48 t-cell activation wd repeat protein. [refseq;acc:nm_139281] 1.10597
4063.64 837 4492.98 cirhin; testis expressed gene 292; cirrhosis, autosomal recessive 1a. [refseq;acc:nm_032830] 1.10565
4064.23 838 4493.36 pbk1 protein. [sptrembl;acc:o76021] 1.10559
4066.56 848 4491.65 wd-repeat protein bing4. [swissprot;acc:o15213] 1.10453
4068.56 181 5252.6 eukaryotic translation initiation factor 4 gamma, 3. [refseq;acc:nm_003760] 1.29102
4068.78 208 5082.18 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]

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/