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.


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 [...,...].
Rank Gene description Value Type Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 6614 to 6663 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
red
green
network_comparison
1654 karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Rooted 61.873 63.9658 1.03382
sterol regulatory element binding protein cleavage-activating protein (srebp cleavage-activating protein) (scap). [swissprot;acc:q12770] Ranked 219.062 215.942 1.01445
transcription factor maff (v-maf musculoaponeurotic fibrosarcoma oncogene homolog f) (u-maf). [swissprot;acc:q9ulx9] Measured 7433.73 7950.61 1.06953
1655 40s ribosomal protein s26. [swissprot;acc:p02383] 5488.7 5131.89
atp synthase beta chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p06576] Ranked 219.062 215.942 1.01445
dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] Squared 14714.1 16283.8 1.10668
proteasome subunit alpha type 2 (ec 3.4.25.1) (proteasome component c3) (macropain subunit c3) (multicatalytic endopeptidase complex subunit c3). [swissprot;acc:p25787] Rooted 64.6548 66.8408 1.03381
1656 dnaj homolog subfamily b member 4 (heat shock 40 kda protein 1 homolog) (heat shock protein 40 homolog) (hsp40 homolog). [swissprot;acc:q9udy4] Squared 23451.3 25948.4 1.10648
importin beta-2 subunit (karyopherin beta-2 subunit) (transportin) (m9 region interaction protein) (mip). [swissprot;acc:q92973] Rooted 61.8671 63.9574 1.03379
mitochondrial import inner membrane translocase subunit tim22. [swissprot;acc:q9y584] Measured 5488.7 5131.89 1.06953
phosphatidylinositol 3-kinase regulatory beta subunit (pi3-kinase p85-beta subunit) (ptdins-3-kinase p85-beta). [swissprot;acc:o00459] Ranked 219.062 215.942 1.01445
1657 atp synthase mitochondrial f1 complex assembly factor 2. [refseq;acc:nm_145691] Measured 5488.7 5131.89 1.06953
cab2. [refseq;acc:nm_033419] Squared 23451.3 25948.4 1.10648
cleavage and polyadenylation specific factor 5, 25 kd subunit; pre-mrna cleavage factor im (25kd); pre-mrna cleavage factor im, 25kd subunit. [refseq;acc:nm_007006] Ranked 219.314 216.195 1.01443
pepsin a precursor (ec 3.4.23.1). [swissprot;acc:p00790] Rooted 54.1965 56.0231 1.0337
1658 atp synthase alpha chain, mitochondrial precursor (ec 3.6.3.14). [swissprot;acc:p25705] Ranked 217.925 214.826 1.01443
dnaj homolog subfamily b member 5 (heat shock protein hsp40-3) (heat shock protein cognate 40) (hsc40) (hsp40-2). [swissprot;acc:o75953] Squared 23451.3 25948.4 1.10648
solute carrier family 20 (phosphate transporter), member 2; glvr-2; pit-2; gibbon ape leukemia virus receptor 2; murine leukemia virus, amphotropic; receptor. [refseq;acc:nm_006749] Rooted 54.1965 56.0231 1.0337
transcription factor mafk (erythroid transcription factor nf-e2 p18 subunit). [swissprot;acc:o60675] Measured 7433.73 7950.61 1.06953
1659 28s ribosomal protein s18a, mitochondrial precursor (mrp-s18-a) (mrps18a) (mrp-s18-3). [swissprot;acc:q9nvs2] Ranked 217.925 214.826 1.01443
dnaj homolog subfamily b member 1 (heat shock 40 kda protein 1) (heat shock protein 40) (hsp40) (dnaj protein homolog 1) (hdj-1). [swissprot;acc:p25685] Squared 23451.3 25948.4 1.10648
farnesyl pyrophosphate synthetase (fpp synthetase) (fps) (farnesyl diphosphate synthetase) [includes: dimethylallyltransferase (ec 2.5.1.1); geranyltranstransferase (ec 2.5.1.10)]. [swissprot;acc:p14324] Rooted 54.1965 56.0231 1.0337
ubiquinol-cytochrome c reductase complex 14 kda protein (ec 1.10.2.2) (complex iii subunit vi) (qp-c). [swissprot;acc:p14927] Measured 5488.7 5131.89 1.06953
1660 cell adhesion molecule with homology to l1cam precursor; neural cell adhesion molecule; cell adhesion molecule l1-like; l1 cell adhesion molecule 2. [refseq;acc:nm_006614] 7433.73 7950.61
early endosome antigen 1, 162kd; early endosome-associated protein. [refseq;acc:nm_003566] Ranked 228.654 231.933 1.01434
eukaryotic peptide chain release factor subunit 1 (erf1) (eukaryotic release factor 1) (tb3-1) (c11 protein). [swissprot;acc:p46055] Squared 23451.3 25948.4 1.10648
protocadherin 15 precursor. [swissprot;acc:q96qu1] Rooted 54.1965 56.0231 1.0337
1661 adenylosuccinate synthase-like 1. [refseq;acc:nm_152328] Ranked 204.437 201.551 1.01432
neural cell adhesion molecule l1 precursor (n-cam l1) (cd171 antigen). [swissprot;acc:p32004] Measured 7433.73 7950.61 1.06953
solute carrier family 20 (phosphate transporter), member 1; glvr-1; pit-1; gibbon ape leukemia virus receptor 1. [refseq;acc:nm_005415] Rooted 54.1965 56.0231 1.0337
suppressor of actin mutations 2-like isoform b; dj1033b10.5. [refseq;acc:nm_022553] Squared 23451.3 25948.4 1.10648
1662 28s ribosomal protein s9, mitochondrial precursor (mrp-s9). [swissprot;acc:p82933] 13992.7 15480.4 1.10632
lipocalin-interacting membrane receptor. [refseq;acc:nm_018113] Rooted 54.1965 56.0231 1.0337
transcription factor-like protein mrgx (morf-related gene x protein) (mortality factor 4-like 2) (msl3-2 protein). [swissprot;acc:q15014] Ranked 228.477 231.747 1.01431
transcription initiation factor tfiid 31 kda subunit (tafii-31) (tafii-32) (tafii32). [swissprot;acc:q16594] Measured 7433.73 7950.61 1.06953
1663 epsin 3. [refseq;acc:nm_017957] Squared 26657.9 29490.6 1.10626
nuclear factor erythroid 2 related factor 1 (nf-e2 related factor 1) (nfe2-related factor 1) (nuclear factor, erythroid derived 2, like 1) (transcription factor 11) (transcription factor hbz17) (transcription factor lcr-f1) (locus control region-factor 1). [swissprot;acc:q14494] Measured 7433.73 7950.61 1.06953
tryptophan 2,3-dioxygenase (ec 1.13.11.11) (tryptophan pyrrolase) (tryptophanase) (tryptophan oxygenase) (tryptamin 2,3-dioxygenase) (trpo). [swissprot;acc:p48775] Ranked 218.335 215.26 1.01429
zinc finger protein gli1 (glioma-associated oncogene) (oncogene gli). [swissprot;acc:p08151] Rooted 54.1965 56.0231 1.0337
1664 nuclear factor (erythroid-derived 2)-like 3; nf-e2-related factor 3. [refseq;acc:nm_004289] Measured 7433.73 7950.61 1.06953
suppressor of fused. [refseq;acc:nm_016169] Rooted 54.1965 56.0231 1.0337
transcription factor-like protein morf4 (mortality factor 4) (cellular senescence-related protein 1) (sen1). [swissprot;acc:q9y690] Ranked 228.484 231.74 1.01425
zinc ribbon domain containing, 1; transcription-associated zinc ribbon protein; rna polymerase i small specific subunit rpa12. [refseq;acc:nm_014596] Squared 16044.8 17746.5 1.10606
1665 adenylosuccinate synthetase (ec 6.3.4.4) (imp--aspartate ligase) (adss) (ampsase). [swissprot;acc:p30520] Ranked 204.433 201.564 1.01423
fatty acid-binding protein, adipocyte (afabp) (adipocyte lipid-binding protein) (albp) (a-fabp). [swissprot;acc:p15090] Measured 5791.14 6193.02 1.0694
mesoderm induction early response 1. [refseq;acc:nm_020948] Squared 29813.9 32974.4 1.10601
zinc finger protein gli3. [swissprot;acc:p10071] Rooted 54.1965 56.0231 1.0337
1666 fatty acid-binding protein, epidermal (e-fabp) (psoriasis-associated fatty acid-binding protein homolog) (pa-fabp). [swissprot;acc:q01469] Measured 5791.14 6193.02 1.0694
karyopherin beta 2b, transportin; importin 3. [refseq;acc:nm_013433] Ranked 218.679 215.612 1.01422
limb region 1 protein; limb region 1. [refseq;acc:nm_022458] Rooted 54.1965 56.0231 1.0337

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/