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 red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1375 to 1424 of 25824 in total
Interaction Map  : High confidence
Filtered  : 1
Rank
description
Value Type
Network Comparison Type
red
green
network_comparison
172 splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] Rooted Divided 56.7592 65.9889 1.16261
trophinin. [swissprot;acc:q12816] Measured 23693.7 18263 1.29736
173 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] Rooted 145.551 168.796 1.1597
breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] Measured 4579.34 5940.64 1.29727
methyltransferase like 2. [refseq;acc:nm_018396] Squared Subtracted 71576.8 56326.7 15250.1
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] Rooted 37.3005 48.4141 11.1136
septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] Squared Divided 82624.3 115061 1.39258
short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] Ranked Subtracted 201.515 228.752 27.237
small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] Divided 227.032 193.056 1.17599
uncharacterized hematopoietic stem/progenitor cells protein mds026. [sptrembl;acc:q9nz48] Measured Subtracted 4556.79 2945.28 1611.51
174 cytoplasmic dynein light chain (t-complex testis-specific protein 1 homolog) (protein cw-1). [swissprot;acc:q15763] Squared 71576.8 56326.7 15250.1
dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] Ranked Divided 335 286 1.17133
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] Subtracted 228.1 200.968 27.132
mad protein (max dimerizer). [swissprot;acc:q05195] Measured Divided 4455.95 5774.03 1.2958
pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] Rooted 145.551 168.796 1.1597
s-phase kinase-associated protein 1a (cyclin a/cdk2-associated protein p19) (p19a) (p19skp1) (rna polymerase ii elongation factor-like protein) (organ of corti protein 2) (ocp-ii protein) (ocp-2) (transcription elongation factor b) (siii). [swissprot;acc:p34991] Subtracted 37.3005 48.4141 11.1136
sedlin. [swissprot;acc:o14582] Squared Divided 112820 157033 1.39189
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, beta isoform (pp2a, subunit b, b-beta isoform) (pp2a, subunit b, b55- beta isoform) (pp2a, subunit b, pr55-beta isoform) (pp2a, subunit b, r2-beta isoform). [swissprot;acc:q00005] Measured Subtracted 4556.83 2945.38 1611.45
175 cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] Ranked Divided 199.949 234.187 1.17123
f-box protein fbw7 isoform 2; archipelago, drosophila, homolog of; f-box protein fbw7; f-box protein sel-10; homolog of c elegans sel-10. [refseq;acc:nm_018315] Rooted Subtracted 37.3005 48.4141 11.1136
fzr1 protein; fizzy-related protein; cdc20-like 1b. [refseq;acc:nm_016263] Squared 71576.8 56326.7 15250.1
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] Ranked 228.085 201.006 27.079
max interacting protein 1 (mxi1 protein). [swissprot;acc:p50539] Measured Divided 4456.67 5773.77 1.29553
pantothenate kinase 2, mitochondrial precursor (ec 2.7.1.33) (pantothenic acid kinase 2) (hpank2). [swissprot;acc:q9bz23] Rooted 145.551 168.796 1.1597
serine/threonine protein phosphatase 2a, 55 kda regulatory subunit b, gamma isoform (pp2a, subunit b, b-gamma isoform) (pp2a, subunit b, b55-gamma isoform) (pp2a, subunit b, pr55-gamma isoform) (pp2a, subunit b, r2-gamma isoform) (imypno1). [swissprot;acc:q9y2t4] Measured Subtracted 4556.99 2945.8 1611.19
synbindin (trs23 homolog) (hematopoietic stem/progenitor cell protein 172) (hspc172) (ptd009) (cgi-104). [swissprot;acc:q9y296] Squared Divided 112820 157033 1.39189
176 bet3 homolog. [swissprot;acc:o43617]
cullin homolog 2 (cul-2). [swissprot;acc:q13617] Rooted Subtracted 37.3005 48.4141 11.1136
dna polymerase epsilon p12 subunit (dna polymerase epsilon subunit 4). [swissprot;acc:q9nr33] Ranked Divided 275.754 235.908 1.1689
eukaryotic translation initiation factor 5 (eif-5). [swissprot;acc:p55010] Subtracted 271.016 244.167 26.849
hypoxanthine-guanine phosphoribosyltransferase (ec 2.4.2.8) (hgprt) (hgprtase). [swissprot;acc:p00492] Measured 10235.2 11830.8 1595.6
max-interacting transcriptional repressor mad4 (max-associated protein 4) (max dimerization protein 4). [swissprot;acc:q14582] Divided 4456.93 5773.67 1.29544
pantothenate kinase 3 (ec 2.7.1.33) (pantothenic acid kinase 3) (hpank3). [swissprot;acc:q9h999] Rooted 145.551 168.796 1.1597
proprotein convertase subtilisin/kexin type 5 precursor (ec 3.4.21.-) (proprotein convertase pc5) (subtilisin/kexin-like protease pc5) (convertase pc5) (pc6) (hpc6). [swissprot;acc:q92824] Squared Subtracted 71576.8 56326.7 15250.1
177 beta-arrestin 2 (arrestin, beta 2). [swissprot;acc:p32121] 9924.76 25146.6 15221.8
dj820b18.1 (similar to nuclear cap binding protein) (fragment). [sptrembl;acc:q8wwk2] Ranked Divided 229.406 196.695 1.1663
lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] Measured Subtracted 4110.14 5694.99 1584.85
max dimerization protein 3; likely ortholog of mouse max dimerization protein 3. [refseq;acc:nm_031300] Divided 4457.06 5773.63 1.29539
mitochondrial solute carrier protein. [refseq;acc:nm_145305] Rooted 145.551 168.796 1.1597
presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] Subtracted 37.3005 48.4141 11.1136
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Squared Divided 78383 108483 1.38401
transcriptional co-repressor sin3a; transcriptional regulator, sin3a (yeast). [refseq;acc:nm_015477] Ranked Subtracted 241.07 267.88 26.81
178 beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] Squared 9924.76 25146.6 15221.8
carboxypeptidase b precursor. [refseq;acc:nm_020361] Divided 25326.4 18354.1 1.37988
cullin homolog 1 (cul-1). [swissprot;acc:q13616] Rooted Subtracted 37.3005 48.4141 11.1136
density-regulated protein (drp) (drp1 protein) (smooth muscle cell associated protein-3) (smap-3). [swissprot;acc:o43583] Ranked 241.07 267.88 26.81
formin binding protein 3; fas-ligand associated factor 1; huntingtin-interacting protein a; ny-ren-6 antigen. [refseq;acc:nm_017892] Divided 226.887 194.72 1.1652
myosin vb (myosin 5b) (fragment). [swissprot;acc:q9ulv0] Measured 21591.5 27904.5 1.29238
stem cell growth factor; lymphocyte secreted c-type lectin; lymphocyte secreted c-type lectin. [refseq;acc:nm_002975] Subtracted 10908.6 12491.8 1583.2
transcription factor dp-2 (e2f dimerization partner 2). [swissprot;acc:q14188] Rooted Divided 45.7414 52.932 1.1572

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/