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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Rank Gene Hugo 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
Hugo
description
Value Type
Interaction Map
red
green
network_comparison
51 GBAS nipsnap2 protein (glioblastoma amplified sequence). [swissprot;acc:o75323] Rooted Low confidence 55.0884 62.0722 1.12677
HOXC5 homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 122475 159767 1.30449
JPH2 junctophilin 2 (junctophilin type 2) (jp-2). [swissprot;acc:q9br39] Ranked 234.802 260.98 1.11149
KHDRBS2 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
NEUROD4 neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1390.33 1.78438
SPATA6 spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 133 105 1.26667
STAMBP associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared 28994.2 17134.8 1.69212
XKR7 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
52 no value homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared 122475 159767 1.30449
AMPD2 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Ranked High confidence 133 105 1.26667
ATG4B cysteine endopeptidase aut-like isoform b. [refseq;acc:nm_178326] Measured Low confidence 13195.9 11486.4 1.14883
CHD5 chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] High confidence 779.167 1390.33 1.78438
NEURL neuralized-like. [refseq;acc:nm_004210] Rooted 27.9107 44.1656 1.58239
NIPSNAP1 nipsnap1 protein. [swissprot;acc:q9bpw8] Low confidence 55.133 62.1073 1.1265
SMPD2 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
VPS24 neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared High confidence 28994.2 17134.8 1.69212
53 BOK bcl2-related ovarian killer. [refseq;acc:nm_032515] Measured Low confidence 4955.33 5659.35 1.14207
CDK2AP1 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
CHMP4A protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared 28994.2 17134.8 1.69212
HOXD4 homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Low confidence 122475 159767 1.30449
JUNB transcription factor jun-b. [swissprot;acc:p17275] Ranked High confidence 201.144 158.868 1.26611
JUND transcription factor jun-d. [swissprot;acc:p17535] Rooted Low confidence 67.1245 75.5619 1.1257
NDUFS4 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] High confidence 30.8986 46.4619 1.50369
TMEM33 db83 protein. [swissprot;acc:p57088] Ranked Low confidence 234.802 260.98 1.11149
54 CPEB3 cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 267.448 240.822 1.11056
DTX2 deltex 2. [refseq;acc:nm_020892] Measured High confidence 1618.84 2651.88 1.63814
HOXB5 homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Squared Low confidence 122475 159767 1.30449
JUNB transcription factor jun-b. [swissprot;acc:p17275] Rooted 67.118 75.5523 1.12566
JUND transcription factor jun-d. [swissprot;acc:p17535] Ranked High confidence 200.941 158.941 1.26425
MAGED4 melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Squared 219048 129762 1.68808
SEPT8 septin-like protein kiaa0202 (fragment). [swissprot;acc:q92599] Measured Low confidence 13203.5 15033.4 1.13859
UFC1 protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Rooted High confidence 40.0958 58.7986 1.46645
55 no value 60s ribosomal protein l37a. [swissprot;acc:p12751] Low confidence 57.2649 64.3669 1.12402
CPEB4 cytoplasmic polyadenylation element binding protein 4. [refseq;acc:nm_030627] Ranked 267.376 240.78 1.11046
DTX1 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured High confidence 1629.21 2662.12 1.63399
HOXA5 homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Squared Low confidence 122475 159767 1.30449
KCND2 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
MAGEE2 hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared 219048 129762 1.68808
PRKRAP1 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
SEPT10 septin 10 isoform 1. [refseq;acc:nm_144710] Measured Low confidence 13081.2 14872.6 1.13694
56 no value guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Ranked High confidence 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
CTH cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 28.9509 1.43986
GSTO2 ba127l20.1 (novel glutathione-s-transferase). [sptrembl;acc:q9h4y5] Low confidence 62.7951 70.575 1.12389
PBK 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 High confidence 1631.67 2664.55 1.63302
T brachyury protein (t protein). [swissprot;acc:o15178] Ranked Low confidence 224.922 202.592 1.11022
57 FOS proto-oncogene protein c-fos (cellular oncogene fos) (g0/g1 switch regulatory protein 7). [swissprot;acc:p01100] 202.802 182.73 1.10985
GNG12 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 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
- Hugo is the HGNC identifier if it exists
- 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/