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 1080 to 1129 of 8289 in total
Value Type  : Measured
Network Comparison Type  : Divided
Filtered  : 1
Rank
description
Interaction Map
red
green
network_comparison
540 pre-mrna splicing factor prp17 (hprp17) (eh-binding protein 3) (ehb3). [swissprot;acc:o60508] Low confidence 7937.69 8310.27 1.04694
541 calsyntenin-2 precursor. [swissprot;acc:q9h4d0] High confidence 10600.3 12065.2 1.13819
dnaj homolog subfamily a member 4. [swissprot;acc:q8ww22] Low confidence 8574.98 8976.82 1.04686
542 heterogeneous nuclear ribonucleoprotein h' (hnrnp h') (ftp-3). [swissprot;acc:p55795] 7305.05 7647.16 1.04683
rac-alpha serine/threonine kinase (ec 2.7.1.-) (rac-pk-alpha) (protein kinase b) (pkb) (c-akt). [swissprot;acc:p31749] High confidence 3889.27 4426.74 1.13819
543 calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 10599.9 12064.7
phosphatidylinositol 4-kinase type-ii beta; likely ortholog of mouse phosphatidylinositol 4-kinase type 2 beta. [refseq;acc:nm_018323] Low confidence 8159.4 8541.33 1.04681
544 pp1201 protein. [refseq;acc:nm_022152] 7723.74 8085.19 1.0468
rac-gamma serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-gamma) (protein kinase akt-3) (protein kinase b, gamma) (pkb gamma) (stk-2). [swissprot;acc:q9y243] High confidence 3889.27 4426.74 1.13819
545 phosphatidylinositol 4-kinase type ii. [refseq;acc:nm_018425] Low confidence 8159.25 8540.75 1.04676
rac-beta serine/threonine protein kinase (ec 2.7.1.-) (rac-pk-beta) (protein kinase akt-2) (protein kinase b, beta) (pkb beta). [swissprot;acc:p31751] High confidence 3889.27 4426.74 1.13819
546 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Low confidence 8451.27 8845.91 1.0467
zinc finger protein t86. [swissprot;acc:o00488] High confidence 4052.77 4612.54 1.13812
547 small glutamine rich protein with tetratricopeptide repeats 2. [refseq;acc:nm_019072] Low confidence 8727.92 9135.42 1.04669
werner helicase interacting protein isoform 1; putative helicase ruvbl; werner helicase interacting protein. [refseq;acc:nm_020135] High confidence 5291.92 6020.19 1.13762
548 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Low confidence 8447.46 8841.77 1.04668
adrenodoxin, mitochondrial precursor (adrenal ferredoxin) (hepatoredoxin) (ferredoxin 1). [swissprot;acc:p10109] High confidence 8268.19 9405.85 1.13759
549 dolichol-phosphate mannosyltransferase (ec 2.4.1.83) (dolichol- phosphate mannose synthase) (dolichyl-phosphate beta-d- mannosyltransferase) (mannose-p-dolichol synthase) (mpd synthase) (dpm synthase). [swissprot;acc:o60762] 5865.79 6671.23 1.13731
imp2 inner mitochondrial membrane protease-like; inner mitochondrial membrane peptidase 2 like. [refseq;acc:nm_032549] Low confidence 7823.38 8187.78 1.04658
550 cytochrome p450 4f8 (ec 1.14.14.1) (cypivf8). [swissprot;acc:p98187] 8132.78 8511.5 1.04657
prohibitin. [swissprot;acc:p35232] High confidence 5773.45 6563.69 1.13687
551 repressor of estrogen receptor activity; b-cell associated protein. [refseq;acc:nm_007273]
sterol regulatory element binding protein-2 (srebp-2) (sterol regulatory element-binding transcription factor 2). [swissprot;acc:q12772] Low confidence 7739.76 8100.23 1.04657
552 cleavage stimulation factor, 64 kda subunit (cstf 64 kda subunit) (cf-1 64 kda subunit). [swissprot;acc:p33240] High confidence 15427.2 13572.8 1.13663
sterol regulatory element binding protein-1 (srebp-1) (sterol regulatory element-binding transcription factor 1). [swissprot;acc:p36956] Low confidence 7739.76 8100.23 1.04657
553 exocyst complex component sec6. [swissprot;acc:o60645] 8385.7 8776.09 1.04655
tgf beta-inducible nuclear protein 1; hairy cell leukemia protein 1. [refseq;acc:nm_014886] High confidence 3853.64 4379.71 1.13651
554 axonemal dynein light intermediate polypeptide 1 (inner dynein arm light chain, axonemal) (hp28). [swissprot;acc:o14645] Low confidence 7296.43 7635.83 1.04652
pre-mrna cleavage complex ii protein clp1. [swissprot;acc:q92989] High confidence 14830.5 13050.3 1.13641
555 peripheral plasma membrane protein cask (ec 2.7.1.-) (hcask) (calcium/calmodulin-dependent serine protein kinase) (lin-2 homolog). [swissprot;acc:o14936] Low confidence 7305.56 7644.68 1.04642
selenide,water dikinase 2 (ec 2.7.9.3) (selenophosphate synthetase 2) (selenium donor protein 2). [swissprot;acc:q99611] High confidence 6167.93 7007.7 1.13615
556 flavoprotein oxidoreductase mical2. [refseq;acc:nm_014632]
wiskott-aldrich syndrome protein interacting protein (wasp interacting protein) (prpl-2 protein). [swissprot;acc:o43516] Low confidence 8139.29 8517.13 1.04642
557 inositol polyphosphate-4-phosphatase, type ii, 105kd; inositol polyphosphate 4-phosphatase ii; 4-phosphatase ii. [refseq;acc:nm_003866] High confidence 6167.93 7007.7 1.13615
single-minded homolog 1. [swissprot;acc:p81133] Low confidence 7305.56 7644.68 1.04642
558 cytochrome p450 4f12 (ec 1.14.14.1) (cypivf12). [swissprot;acc:q9hcs2] 8130.02 8507.23 1.0464
selenide,water dikinase 1 (ec 2.7.9.3) (selenophosphate synthetase 1) (selenium donor protein 1). [swissprot;acc:p49903] High confidence 6167.93 7007.7 1.13615
559 inositol polyphosphate-4-phosphatase, type 1 isoform b; inositol polyphosphate-4-phosphatase, type i, 107kd; 4-phosphatase i; inositol polyphosphate-4-phosphatase i. [refseq;acc:nm_001566]
son of sevenless protein homolog 1 (sos-1). [swissprot;acc:q07889] Low confidence 8069.31 8443.5 1.04637
560 amp deaminase 2 (ec 3.5.4.6) (amp deaminase isoform l). [swissprot;acc:q01433] 7980.85 8350.82 1.04636
cystathionine beta-synthase (ec 4.2.1.22) (serine sulfhydrase) (beta-thionase). [swissprot;acc:p35520] High confidence 5480.24 6222.04 1.13536
561 lifeguard; kiaa0950 protein. [refseq;acc:nm_012306] Low confidence 7755.77 8115.27 1.04635
transforming protein rhoc (h9). [swissprot;acc:p08134] High confidence 5480.24 6222.04 1.13536
562 conserved oligomeric golgi complex component 3 (vesicle docking protein sec34 homolog) (p94). [swissprot;acc:q96jb2] Low confidence 7561.22 7911.04 1.04627
thiosulfate sulfurtransferase (ec 2.8.1.1) (rhodanese). [swissprot;acc:q16762] High confidence 5480.24 6222.04 1.13536
563 3-mercaptopyruvate sulfurtransferase (ec 2.8.1.2) (mst). [swissprot;acc:p25325]
cytochrome p450 4f3 (ec 1.14.13.30) (cypivf3) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:q08477] Low confidence 8126.42 8502.33 1.04626
564 cytochrome p450 4f2 (ec 1.14.13.30) (cypivf2) (leukotriene-b4 omega- hydroxylase) (leukotriene-b4 20-monooxygenase) (cytochrome p450- ltb-omega). [swissprot;acc:p78329] 8125.5 8501.28 1.04625
transforming protein rhoa (h12). [swissprot;acc:p06749] High confidence 5480.24 6222.04 1.13536
565 cytochrome p450 4f11 (ec 1.14.14.1) (cypivf11). [swissprot;acc:q9hbi6] Low confidence 8126.71 8502.61 1.04625

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/