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 description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
51 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Squared Divided 28994.2 17134.8 1.69212
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Ranked Subtracted 350 290 60
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 23640.2 19479.8 4160.4
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Rooted 137.446 120.823 16.623
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Squared 173408 242989 69581
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Rooted Divided 27.7254 44.0299 1.58807
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 779.167 1390.33 1.78438
spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 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
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 23422.4 19380.3 4042.1
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 173408 242989 69581
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 137.446 120.823 16.623
neuralized-like. [refseq;acc:nm_004210] Divided 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
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Ranked Subtracted 350 290 60
53 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] Measured Divided 779.167 1390.33 1.78438
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Squared Subtracted 173408 242989 69581
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] Ranked 318.982 259.004 59.978
Rooted Divided 30.8986 46.4619 1.50369
necdin. [swissprot;acc:q99608] Subtracted 137.446 120.823 16.623
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 23326.5 19296.4 4030.1
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Squared Divided 28994.2 17134.8 1.69212
transcription factor jun-b. [swissprot;acc:p17275] Ranked 201.144 158.868 1.26611
54 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Subtracted 185.678 245.247 59.569
deltex 2. [refseq;acc:nm_020892] Measured Divided 1618.84 2651.88 1.63814
exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 23316 19288.8 4027.2
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared 173408 242989 69581
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 219048 129762 1.68808
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Rooted Subtracted 137.446 120.823 16.623
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 40.0958 58.7986 1.46645
transcription factor jun-d. [swissprot;acc:p17535] Ranked 200.941 158.941 1.26425
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured 1629.21 2662.12 1.63399
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Ranked Subtracted 185.678 245.247 59.569
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Squared Divided 219048 129762 1.68808
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted 173408 242989 69581
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Rooted 137.446 120.823 16.623
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Measured 23303.1 19279.5 4023.6
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Rooted Divided 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
56 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 41.6851 28.9509 1.43986
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Ranked Subtracted 185.678 245.247 59.569
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Divided 266.856 336.233 1.25998
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Squared Subtracted 173408 242989 69581
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Rooted 137.446 120.823 16.623
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Squared Divided 219048 129762 1.68808
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Measured Subtracted 20911 24908.5 3997.5
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] Divided 1631.67 2664.55 1.63302
57 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked 266.856 336.233 1.25998
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Squared Subtracted 173408 242989 69581

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/