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 Value Type description 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
Value Type
description
Network Comparison Type
red
green
network_comparison
51 Measured fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Subtracted 23640.2 19479.8 4160.4
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Divided 779.167 1390.33 1.78438
Ranked cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Subtracted 350 290 60
spermatogenesis associated 6. [refseq;acc:nm_019073] Divided 133 105 1.26667
Squared associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 28994.2 17134.8 1.69212
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Subtracted 173408 242989 69581
Rooted hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] 137.446 120.823 16.623
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided 27.7254 44.0299 1.58807
52 Measured chromodomain helicase dna binding protein 5. [refseq;acc:nm_015557] 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
Ranked amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] Divided 133 105 1.26667
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted 350 290 60
Squared homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] 173408 242989 69581
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Divided 28994.2 17134.8 1.69212
Rooted melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Subtracted 137.446 120.823 16.623
neuralized-like. [refseq;acc:nm_004210] Divided 27.9107 44.1656 1.58239
53 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] 779.167 1390.33 1.78438
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Subtracted 23326.5 19296.4 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] 318.982 259.004 59.978
transcription factor jun-b. [swissprot;acc:p17275] Divided 201.144 158.868 1.26611
Squared homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted 173408 242989 69581
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided 28994.2 17134.8 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] 30.8986 46.4619 1.50369
necdin. [swissprot;acc:q99608] Subtracted 137.446 120.823 16.623
54 Measured deltex 2. [refseq;acc:nm_020892] Divided 1618.84 2651.88 1.63814
exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 23316 19288.8 4027.2
Ranked 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] 185.678 245.247 59.569
transcription factor jun-d. [swissprot;acc:p17535] Divided 200.941 158.941 1.26425
Squared homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Subtracted 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
Rooted melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted 137.446 120.823 16.623
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 40.0958 58.7986 1.46645
55 Measured deltex homolog 1; hdx-1. [refseq;acc:nm_004416] 1629.21 2662.12 1.63399
poly(a) polymerase gamma (ec 2.7.7.19) (pap gamma) (polynucleotide adenylyltransferase gamma) (srp rna 3' adenylating enzyme). [swissprot;acc:q9bwt3] Subtracted 23303.1 19279.5 4023.6
Ranked glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] 185.678 245.247 59.569
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Divided 320.927 254.434 1.26134
Squared hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] 219048 129762 1.68808
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted 173408 242989 69581
Rooted melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] 137.446 120.823 16.623
potassium voltage-gated channel, shal-related subfamily, member 2; voltage-sensitive potassium channel; voltage-gated potassium channel kv4.2. [refseq;acc:nm_012281] Divided 41.6734 28.9323 1.44038
56 Measured ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] 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
Ranked glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] 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
Squared homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted 173408 242989 69581
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided 219048 129762 1.68808
Rooted cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] 41.6851 28.9509 1.43986
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Subtracted 137.446 120.823 16.623
57 Measured kh domain containing, rna binding, signal transduction associated 3; sam68-like phosphotyrosine protein, t-star. [refseq;acc:nm_006558] Divided 1631.67 2664.55 1.63302
ras-related gtp binding c; rag c protein. [refseq;acc:nm_022157] Subtracted 20911 24908.5 3997.5

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/