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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Gene Rank Network Comparison Type Value Type description green Interaction Map red Filtered network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
Network Comparison Type
Value Type
description
green
red
network_comparison
51 Divided Measured neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] 1390.33 779.167 1.78438
Ranked spermatogenesis associated 6. [refseq;acc:nm_019073] 105 133 1.26667
Squared associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 17134.8 28994.2 1.69212
Rooted kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] 44.0299 27.7254 1.58807
Subtracted Measured fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] 19479.8 23640.2 4160.4
Ranked cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] 290 350 60
Squared homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] 242989 173408 69581
Rooted hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 120.823 137.446 16.623
52 Divided Measured chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 1390.33 779.167 1.78438
Ranked amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 105 133 1.26667
Squared neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] 17134.8 28994.2 1.69212
Rooted neuralized-like. [refseq;acc:nm_004210] 44.1656 27.9107 1.58239
Subtracted Measured cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] 19380.3 23422.4 4042.1
Ranked ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] 290 350 60
Squared homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 242989 173408 69581
Rooted melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] 120.823 137.446 16.623
53 Divided Measured 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] 1390.33 779.167 1.78438
Ranked transcription factor jun-b. [swissprot;acc:p17275] 158.868 201.144 1.26611
Squared protein hspc134 (protein cda04). [swissprot;acc:q9by43] 17134.8 28994.2 1.69212
Rooted 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] 46.4619 30.8986 1.50369
Subtracted Measured poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] 19296.4 23326.5 4030.1
Ranked 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] 259.004 318.982 59.978
Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] 242989 173408 69581
Rooted necdin. [swissprot;acc:q99608] 120.823 137.446 16.623
54 Divided Measured deltex 2. [refseq;acc:nm_020892] 2651.88 1618.84 1.63814
Ranked transcription factor jun-d. [swissprot;acc:p17535] 158.941 200.941 1.26425
Squared melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] 129762 219048 1.68808
Rooted protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] 58.7986 40.0958 1.46645
Subtracted Measured exocyst complex component sec5. [swissprot;acc:q96kp1] 19288.8 23316 4027.2
Ranked 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 245.247 185.678 59.569
Squared homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] 242989 173408 69581
Rooted melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] 120.823 137.446 16.623
55 Divided Measured deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 2662.12 1629.21 1.63399
Ranked protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] 254.434 320.927 1.26134
Squared hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 129762 219048 1.68808
Rooted potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] 28.9323 41.6734 1.44038
Subtracted Measured poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] 19279.5 23303.1 4023.6
Ranked glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 245.247 185.678 59.569
Squared homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] 242989 173408 69581
Rooted melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 120.823 137.446 16.623
56 Divided Measured 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] 2664.55 1631.67 1.63302
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] 336.233 266.856 1.25998
Squared melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] 129762 219048 1.68808
Rooted cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 28.9509 41.6851 1.43986
Subtracted Measured ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 24908.5 20911 3997.5
Ranked glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 245.247 185.678 59.569
Squared homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] 242989 173408 69581
Rooted melanoma antigen, family b, 6. [refseq;acc:nm_173523] 120.823 137.446 16.623
57 Divided Measured kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] 2664.55 1631.67 1.63302
Ranked guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] 336.233 266.856 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/