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.


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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 401 to 450 of 33156 in total
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Value Type
Interaction Map
red
green
network_comparison
51 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared High confidence 28994.2 17134.8 1.69212
dj310o13.4 (novel protein similar to predicted c. elegans and c. intestinalis proteins) (fragment). [sptrembl;acc:q9nug5] Measured Low confidence 7563.09 8732.2 1.15458
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 122475 159767 1.30449
junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Ranked 234.802 260.98 1.11149
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Rooted High confidence 27.7254 44.0299 1.58807
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1390.33 1.78438
nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] Rooted Low confidence 55.0884 62.0722 1.12677
spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked High confidence 133 105 1.26667
52 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433]
chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] Measured 779.167 1390.33 1.78438
cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Low confidence 13195.9 11486.4 1.14883
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared 122475 159767 1.30449
neuralized-like. [refseq;acc:nm_004210] Rooted High confidence 27.9107 44.1656 1.58239
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 28994.2 17134.8 1.69212
nipsnap1 protein. [swissprot;acc:q9bpw8] Rooted Low confidence 55.133 62.1073 1.1265
sphingomyelin phosphodiesterase 2 (ec 3.1.4.12) (neutral sphingomyelinase) (nsmase) (n-smase) (lyso-platelet activating factor- phospholipase c) (lyso-paf-plc). [swissprot;acc:o60906] Ranked 234.802 260.98 1.11149
53 bcl2-related ovarian killer. [refseq;acc:nm_032515] Measured 4955.33 5659.35 1.14207
cyclin-dependent kinase 2-associated protein 1 (cdk2-associated protein 1) (putative oral cancer suppressor) (deleted in oral cancer- 1) (doc-1). [swissprot;acc:o14519] High confidence 779.167 1390.33 1.78438
db83 protein. [swissprot;acc:p57088] Ranked Low confidence 234.802 260.98 1.11149
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared 122475 159767 1.30449
nadh-ubiquinone oxidoreductase 18 kda subunit, mitochondrial precursor (ec 1.6.5.3) (ec 1.6.99.3) (complex i-18 kda) (ci-18 kda) (complex i- aqdq) (ci-aqdq). [swissprot;acc:o43181] Rooted High confidence 30.8986 46.4619 1.50369
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 17134.8 1.69212
transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 158.868 1.26611
transcription factor jun-d. [swissprot;acc:p17535] Rooted Low confidence 67.1245 75.5619 1.1257
54 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked 267.448 240.822 1.11056
deltex 2. [refseq;acc:nm_020892] Measured High confidence 1618.84 2651.88 1.63814
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared Low confidence 122475 159767 1.30449
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] High confidence 219048 129762 1.68808
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted 40.0958 58.7986 1.46645
septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Low confidence 13203.5 15033.4 1.13859
transcription factor jun-b. [swissprot;acc:p17275] Rooted 67.118 75.5523 1.12566
transcription factor jun-d. [swissprot;acc:p17535] Ranked High confidence 200.941 158.941 1.26425
55 60s ribosomal protein l37a. [swissprot;acc:p12751] Rooted Low confidence 57.2649 64.3669 1.12402
cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Ranked 267.376 240.78 1.11046
deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured High confidence 1629.21 2662.12 1.63399
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared 219048 129762 1.68808
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Low confidence 122475 159767 1.30449
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Rooted High confidence 41.6734 28.9323 1.44038
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked 320.927 254.434 1.26134
septin 10 isoform 1. [refseq;acc:nm_144710] Measured Low confidence 13081.2 14872.6 1.13694
56 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Rooted 62.7951 70.575 1.12389
brachyury protein (t protein). [swissprot;acc:o15178] Ranked 224.922 202.592 1.11022
cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted High confidence 41.6851 28.9509 1.43986
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Ranked 266.856 336.233 1.25998
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared Low confidence 122475 159767 1.30449
homeobox protein hox-c4 (hox-3e) (cp19). [swissprot;acc:p09017] Measured 15464.1 17572.7 1.13635
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Squared High confidence 219048 129762 1.68808
t-lak cell-originated protein kinase; spermatogenesis-related protein kinase; pdz-binding kinase; pbk; mapkk-like protein kinase; serine/threonine protein kinase. [refseq;acc:nm_018492] Measured 1631.67 2664.55 1.63302
57 glutathione transferase omega 1 (ec 2.5.1.18) (gsto 1-1). [swissprot;acc:p78417] Rooted Low confidence 63.0631 70.6746 1.1207
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked High confidence 266.856 336.233 1.25998

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/