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 408 to 457 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
description
Filtered
red
green
network_comparison
204 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 1 201.515 228.752 1.13516
205 60s ribosomal protein l23a. [swissprot;acc:p29316] 0 11844.9 10636.3 1.11363
luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 1 228.1 200.968 1.13501
206 hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] 0 7479 6716 1.11361
luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 1 228.085 201.006 1.13472
207 dc11 protein. [refseq;acc:nm_020186] 0 7479 6716 1.11361
presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 1 285.684 252.234 1.13261
208 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 0 11846.3 10638.4 1.11354
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] 1 285.684 252.234 1.13261
209 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]
small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 0 775 696 1.11351
210 cullin homolog 2 (cul-2). [swissprot;acc:q13617] 1 285.684 252.234 1.13261
mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 0 17144.8 15405.6 1.11289
211 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 1 285.684 252.234 1.13261
ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 0 10367 9320.25 1.11231
212 cullin homolog 1 (cul-1). [swissprot;acc:q13616] 1 285.684 252.234 1.13261
metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] 0 18241.7 16405 1.11196
213 pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 1 210.693 186.95 1.127
protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 0 9379.47 8436.39 1.11179
214 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 1 191.644 170.192 1.12605
probable glutamyl-trna(gln) amidotransferase subunit b, mitochondrial precursor (ec 6.3.5.-) (glu-adt subunit b) (cytochrome oxidase assembly factor pet112 homolog). [swissprot;acc:o75879] 0 7621.99 8473.85 1.11176
215 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 1 112 126 1.125
myosin vi. [swissprot;acc:q9um54] 0 10121.5 11250.5 1.11154
216 maleylacetoacetate isomerase (ec 5.2.1.2) (maai) (glutathione s- transferase zeta 1) (ec 2.5.1.18) (gstz1-1). [swissprot;acc:o43708] 10559.7 11732 1.11102
myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 1 112 126 1.125
217 baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 0 7101.79 6406.18 1.10858
myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 1 112 126 1.125
218 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 0 19355 17469.2 1.10795
myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 1 112 126 1.125
219 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055]
succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 0 12196.2 11009.7 1.10777
220 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 1 112 126 1.125
neurocalcin delta. [swissprot;acc:p29554] 0 13973.6 15473.5 1.10734
221 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 12190.3 13497.2 1.10721
myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 1 112 126 1.125
222 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 0 12183 11013.2 1.10622
dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 1 112 126 1.125
223 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3]
pnas-18. [sptrembl;acc:q9bzu3] 0 12602.7 13939.6 1.10608
224 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 9815.6 8889.93 1.10413
oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 1 185.969 165.623 1.12285
225 40s ribosomal protein s29. [swissprot;acc:p30054] 0 11035.3 9997.71 1.10378
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 1 226.471 201.769 1.12243
226 cartilage oligomeric matrix protein precursor (comp). [swissprot;acc:p49747] 239.991 269.238 1.12187
rab gdp dissociation inhibitor alpha (rab gdi alpha) (gdi-1) (xap-4) (oligophrenin 2). [swissprot;acc:p31150] 0 15395.7 16992.9 1.10374
227 thrombospondin 3 precursor. [swissprot;acc:p49746] 1 239.99 269.234 1.12186
tigger transposable element derived 6. [refseq;acc:nm_030953] 0 12360 11200.2 1.10355
228 sh2 domain containing 3c; novel sh2-containing protein 3; sh2 domain-containing 3c; likely ortholog of mouse cas/hef1-associated signal transducer. [refseq;acc:nm_005489] 1 226.411 202.088 1.12036
soluble liver antigen/liver pancreas antigen. [refseq;acc:nm_153825] 0 10303.5 11370.4 1.10355
229 breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] 1 226.401 202.094 1.12028

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/