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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank description Network Comparison Type Interaction Map Value Type Filtered green red network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Network Comparison Type
Value Type
green
red
network_comparison
51 associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] Divided Squared 17134.8 28994.2 1.69212
cytoplasmic polyadenylation element binding protein 3. [refseq;acc:nm_014912] Subtracted Ranked 290 350 60
fip1-like 1; rearranged in hypereosinophilia. [refseq;acc:nm_030917] Measured 19479.8 23640.2 4160.4
hepatocellular carcinoma-associated protein hca1. [refseq;acc:nm_020932] Rooted 120.823 137.446 16.623
homeobox protein hox-b4 (hox-2f) (hox-2.6). [swissprot;acc:p17483] Squared 242989 173408 69581
kh domain-containing, rna-binding, signal transduction-associated protein 2; sam68-like mammalian protein 1. [refseq;acc:nm_152688] Divided Rooted 44.0299 27.7254 1.58807
neurogenic differentiation factor 4 (neurod4). [swissprot;acc:q9hd90] Measured 1390.33 779.167 1.78438
spermatogenesis associated 6. [refseq;acc:nm_019073] Ranked 105 133 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 1390.33 779.167 1.78438
cleavage and polyadenylation specificity factor, 73 kda subunit (cpsf 73 kda subunit). [swissprot;acc:q9ukf6] Subtracted 19380.3 23422.4 4042.1
homeobox protein hox-c5 (hox-3d) (cp11). [swissprot;acc:q00444] Squared 242989 173408 69581
melanoma-associated antigen 6 (mage-6 antigen) (mage3b). [swissprot;acc:p43360] Rooted 120.823 137.446 16.623
neuralized-like. [refseq;acc:nm_004210] Divided 44.1656 27.9107 1.58239
neuroendocrine differentiation factor; comparative gene identification transcript 149. [refseq;acc:nm_016079] Squared 17134.8 28994.2 1.69212
ras gtpase-activating protein ngap (ras protein activator like 1). [swissprot;acc:q9ujf2] Subtracted Ranked 290 350 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] Divided Measured 1390.33 779.167 1.78438
homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [swissprot;acc:p09630] Subtracted Squared 242989 173408 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] Divided Rooted 46.4619 30.8986 1.50369
Subtracted Ranked 259.004 318.982 59.978
necdin. [swissprot;acc:q99608] Rooted 120.823 137.446 16.623
poly(a) polymerase alpha (ec 2.7.7.19) (pap) (polynucleotide adenylyltransferase alpha) (fragment). [swissprot;acc:p51003] Measured 19296.4 23326.5 4030.1
protein hspc134 (protein cda04). [swissprot;acc:q9by43] Divided Squared 17134.8 28994.2 1.69212
transcription factor jun-b. [swissprot;acc:p17275] Ranked 158.868 201.144 1.26611
54 1,4-alpha-glucan branching enzyme (ec 2.4.1.18) (glycogen branching enzyme) (brancher enzyme). [swissprot;acc:q04446] Subtracted 245.247 185.678 59.569
deltex 2. [refseq;acc:nm_020892] Divided Measured 2651.88 1618.84 1.63814
exocyst complex component sec5. [swissprot;acc:q96kp1] Subtracted 19288.8 23316 4027.2
homeobox protein hox-d4 (hox-4b) (hox-5.1) (hho.c13). [swissprot;acc:p09016] Squared 242989 173408 69581
melanoma antigen, family d, 4 isoform 1; mage1 protein; mage-e1 protein; maged4 protein. [refseq;acc:nm_030801] Divided 129762 219048 1.68808
melanoma-associated antigen d1 (mage-d1 antigen) (neurotrophin receptor-interacting mage homolog) (pro2292). [swissprot;acc:q9y5v3] Subtracted Rooted 120.823 137.446 16.623
protein cgi-126 (protein hspc155). [swissprot;acc:q9y3c8] Divided 58.7986 40.0958 1.46645
transcription factor jun-d. [swissprot;acc:p17535] Ranked 158.941 200.941 1.26425
55 deltex homolog 1; hdx-1. [refseq;acc:nm_004416] Measured 2662.12 1629.21 1.63399
glycogen phosphorylase, brain form (ec 2.4.1.1). [swissprot;acc:p11216] Subtracted Ranked 245.247 185.678 59.569
hepatocellular carcinoma-associated protein hca3. [refseq;acc:nm_138703] Divided Squared 129762 219048 1.68808
homeobox protein hox-b5 (hox-2a) (hho.c10) (hu-1). [swissprot;acc:p09067] Subtracted 242989 173408 69581
melanoma-associated antigen f1 (mage-f1 antigen). [swissprot;acc:q9hay2] Rooted 120.823 137.446 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 19279.5 23303.1 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] Divided Rooted 28.9323 41.6734 1.44038
protein kinase, interferon-inducible double stranded rna dependent activator; protein activator of the interferon-induced protein kinase. [refseq;acc:nm_003690] Ranked 254.434 320.927 1.26134
56 cystathionine gamma-lyase (ec 4.4.1.1) (gamma-cystathionase). [swissprot;acc:p32929] Rooted 28.9509 41.6851 1.43986
glycogen phosphorylase, liver form (ec 2.4.1.1). [swissprot;acc:p06737] Subtracted Ranked 245.247 185.678 59.569
guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-7 subunit. [swissprot;acc:o60262] Divided 336.233 266.856 1.25998
homeobox protein hox-a5 (hox-1c). [swissprot;acc:p20719] Subtracted Squared 242989 173408 69581
melanoma antigen, family b, 6. [refseq;acc:nm_173523] Rooted 120.823 137.446 16.623
melanoma-associated antigen 3 (mage-3 antigen) (antigen mz2-d). [swissprot;acc:p43357] Divided Squared 129762 219048 1.68808
ras-related gtp binding a; ras-related gtp-binding protein. [refseq;acc:nm_006570] Subtracted Measured 24908.5 20911 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 2664.55 1631.67 1.63302
57 guanine nucleotide-binding protein g(i)/g(s)/g(o) gamma-12 subunit. [swissprot;acc:q9ubi6] Ranked 336.233 266.856 1.25998
homeobox protein hox-a4 (hox-1d) (hox-1.4). [swissprot;acc:q00056] Subtracted Squared 242989 173408 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/