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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Value Type Rank Gene Filtered description Network Comparison Type Interaction Map red green network_comparison
Results: HTML CSV LaTeX Showing element 401 to 450 of 3730 in total
Value Type  : Ranked
Network Comparison Type  : Divided
Interaction Map  : High confidence
Rank
Filtered
description
red
green
network_comparison
201 0 maspin precursor (protease inhibitor 5). [swissprot;acc:p36952] 16853 15123 1.1144
1 splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 240.133 211.382 1.13601
202 0 serpin b11. [swissprot;acc:q96p15] 16853 15123 1.1144
1 short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 201.478 228.784 1.13553
203 0 cytoplasmic antiproteinase 2 (cap2) (cap-2) (protease inhibitor 8) (serpin b8). [swissprot;acc:p50452] 16853 15123 1.1144
1 ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 201.515 228.752 1.13516
204 0 dipeptidyl peptidase 8 isoform 2; dipeptidyl peptidase 8. [refseq;acc:nm_017743] 15081.8 16802.1 1.11406
1 short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 201.515 228.752 1.13516
205 0 60s ribosomal protein l23a. [swissprot;acc:p29316] 11844.9 10636.3 1.11363
1 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 228.1 200.968 1.13501
206 0 hepatitis c virus core-binding protein 6; cervical cancer oncogene 3. [refseq;acc:nm_023934] 7479 6716 1.11361
1 luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 228.085 201.006 1.13472
207 0 dc11 protein. [refseq;acc:nm_020186] 7479 6716 1.11361
1 presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 285.684 252.234 1.13261
208 0 c367g8.3 (novel protein similar to rpl23a (60s ribosomal protein l23a)) (60s ribosomal protein l23a like). [sptrembl;acc:q9br02] 11846.3 10638.4 1.11354
1 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] 285.684 252.234 1.13261
209 0 small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 775 696 1.11351
1 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] 285.684 252.234 1.13261
210 0 mms19-like (met18 homolog, s. cerevisiae); homolog of yeast mms19; mms19 (met18 s. cerevisiae)-like. [refseq;acc:nm_022362] 17144.8 15405.6 1.11289
1 cullin homolog 2 (cul-2). [swissprot;acc:q13617] 285.684 252.234 1.13261
211 0 ribosomal protein s6 kinase-like 1. [refseq;acc:nm_031464] 10367 9320.25 1.11231
1 presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 285.684 252.234 1.13261
212 0 metabotropic glutamate receptor 3 precursor (mglur3). [swissprot;acc:q14832] 18241.7 16405 1.11196
1 cullin homolog 1 (cul-1). [swissprot;acc:q13616] 285.684 252.234 1.13261
213 0 protein disulfide isomerase precursor (pdi) (ec 5.3.4.1) (prolyl 4- hydroxylase beta subunit) (cellular thyroid hormone binding protein) (p55). [swissprot;acc:p07237] 9379.47 8436.39 1.11179
1 pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 210.693 186.95 1.127
214 0 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] 7621.99 8473.85 1.11176
1 lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 191.644 170.192 1.12605
215 0 myosin vi. [swissprot;acc:q9um54] 10121.5 11250.5 1.11154
1 myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 112 126 1.125
216 0 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
1 myosin heavy chain, skeletal muscle, fetal (myosin heavy chain iib) (myhc-iib). [swissprot;acc:q9y623] 112 126 1.125
217 0 baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] 7101.79 6406.18 1.10858
1 myosin heavy chain, skeletal muscle, perinatal (myhc-perinatal). [swissprot;acc:p13535] 112 126 1.125
218 0 lim domain binding 1; carboxy terminal lim domain protein 2; lim domain-binding factor-1. [refseq;acc:nm_003893] 19355 17469.2 1.10795
1 myosin heavy chain, skeletal muscle, adult 2 (myosin heavy chain iia) (myhc-iia). [swissprot;acc:q9ukx2] 112 126 1.125
219 0 succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial precursor (ec 1.3.5.1) (fp) (flavoprotein subunit of complex ii). [swissprot;acc:p31040] 12196.2 11009.7 1.10777
1 myosin heavy chain, fast skeletal muscle, embryonic (muscle embryonic myosin heavy chain) (smhce). [swissprot;acc:p11055] 112 126 1.125
220 0 neurocalcin delta. [swissprot;acc:p29554] 13973.6 15473.5 1.10734
1 myosin heavy chain, skeletal muscle, adult 1 (myosin heavy chain iix/d) (myhc-iix/d). [swissprot;acc:p12882] 112 126 1.125
221 0 estrogen-related receptor gamma (estrogen receptor related protein 3) (err gamma-2). [swissprot;acc:o75454] 12190.3 13497.2 1.10721
1 myosin heavy chain, cardiac muscle beta isoform (myhc-beta). [swissprot;acc:p12883] 112 126 1.125
222 0 40s ribosomal protein s15 (rig protein). [swissprot;acc:p11174] 12183 11013.2 1.10622
1 dj756n5.1.1 (continues in em:al133324 as dj1161h23.3) (fragment). [sptrembl;acc:q9h430] 112 126 1.125
223 0 pnas-18. [sptrembl;acc:q9bzu3] 12602.7 13939.6 1.10608
1 myosin heavy chain, skeletal muscle, extraocular (myhc-eo). [swissprot;acc:q9ukx3] 112 126 1.125
224 0 atp-dependent clp protease atp-binding subunit clpx-like, mitochondrial precursor. [swissprot;acc:o76031] 9815.6 8889.93 1.10413
1 oligopeptide transporter, kidney isoform (peptide transporter 2) (kidney h+/peptide cotransporter) (solute carrier family 15, member 2). [swissprot;acc:q16348] 185.969 165.623 1.12285
225 0 40s ribosomal protein s29. [swissprot;acc:p30054] 11035.3 9997.71 1.10378
1 small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] 226.471 201.769 1.12243

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/