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 5508 to 5557 of 29840 in total
Interaction Map  : High confidence
Rank
description
Value Type
Network Comparison Type
Filtered
red
green
network_comparison
345 kinesin-like protein kif13b (kinesin-like protein gakin). [swissprot;acc:q9nqt8] Measured Subtracted 0 957.833 898.833 59
putative pre-mrna splicing factor rna helicase (deah box protein 15) (atp-dependent rna helicase #46). [swissprot;acc:o43143] Rooted Divided 1 56.2615 62.2958 1.10725
ras-related c3 botulinum toxin substrate 1 (p21-rac1) (ras-like protein tc25). [swissprot;acc:p15154] Squared Subtracted 0 346.699 309.317 37.382
retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] Measured Divided 1 20446.1 24136.4 1.18049
sh3-containing grb2-like protein 1 (sh3 domain protein 2b) (extra eleven-nineteen leukemia fusion gene) (een) (een fusion partner of mll). [swissprot;acc:q99961] Squared 35793 44595.3 1.24592
splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] Ranked Subtracted 224.445 204.044 20.401
tbp-associated factor 9l; neuronal cell death-related protein; taf9-like rna polymerase ii, tata box binding protein (tbp)-associated factor, 31 kd; neuronal cell death-related gene in neuron-7; transcription associated factor tafii31l; transcription initiation factor iid, 31kd subunit. [refseq;acc:nm_015975] Squared Divided 0 354.23 402.944 1.13752
transcription factor mafg (v-maf musculoaponeurotic fibrosarcoma oncogene homolog g) (hmaf). [swissprot;acc:o15525] Rooted Subtracted 13.0249 14.2577 1.2328
u2 small nuclear ribonucleoprotein a' (u2 snrnp-a'). [swissprot;acc:p09661] 1 57.9068 64.8562 6.9494
ump-cmp kinase (ec 2.7.4.14) (cytidylate kinase) (deoxycytidylate kinase) (cytidine monophosphate kinase). [swissprot;acc:p30085] Ranked Divided 242.14 265.697 1.09729
vinexin (sh3-containing adaptor molecule-1) (scam-1). [swissprot;acc:o60504] Squared Subtracted 29160.4 35570.2 6409.8
voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] Measured 4068.78 5082.18 1013.4
williams-beuren syndrome chromosome region 14 protein (ws basic-helix- loop-helix leucine zipper protein) (ws-bhlh) (mlx interactor). [swissprot;acc:q9np71] Rooted Divided 0 30.6431 29.1204 1.05229
346 3-ketoacyl-coa thiolase, peroxisomal precursor (ec 2.3.1.16) (beta- ketothiolase) (acetyl-coa acyltransferase) (peroxisomal 3-oxoacyl- coa thiolase). [swissprot;acc:p09110] Measured 1837.26 1721.76 1.06708
40s ribosomal protein s3. [swissprot;acc:p23396] Ranked 1 241.612 265.119 1.09729
apical-like protein (apxl protein). [swissprot;acc:q13796] Subtracted 231.492 211.136 20.356
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] Squared Divided 0 176989 155919 1.13513
dimethylaniline monooxygenase [n-oxide forming] 3 (ec 1.14.13.8) (hepatic flavin-containing monooxygenase 3) (fmo 3) (dimethylaniline oxidase 3) (fmo form 2) (fmo ii). [swissprot;acc:p31513] Measured Subtracted 628.072 686.693 58.621
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Rooted Divided 21.4045 20.3439 1.05213
grb2-related adaptor protein. [swissprot;acc:q13588] 1 61.4282 68.0107 1.10716
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Ranked Subtracted 0 11149.7 10571.4 578.3
importin-alpha re-exporter (chromosome segregation 1-like protein) (cellular apoptosis susceptibility protein). [swissprot;acc:p55060] Squared Divided 1 34018.3 42373 1.24559
ran-binding protein 2-like 1 isoform 2; sperm membrane protein bs-63; ran-binding protein 2-like 1. [refseq;acc:nm_032260] Rooted Subtracted 0 30.2858 31.5117 1.2259
ras-related c3 botulinum toxin substrate 3 (p21-rac3). [swissprot;acc:o14658] Squared 346.699 309.317 37.382
rna polymerase i transcription factor rrn3. [refseq;acc:nm_018427] Ranked Divided 9267.81 9736.2 1.05054
septin 1 (larp) (serologically defined breast cancer antigen ny-br- 24). [swissprot;acc:q8wyj6] Measured 1 14229.2 16780.7 1.17931
splicing factor 3a subunit 2 (spliceosome associated protein 62) (sap 62) (sf3a66). [swissprot;acc:q15428] Rooted Subtracted 57.9819 64.9302 6.9483
vav proto-oncogene. [swissprot;acc:p15498] Squared 31223.8 37614.3 6390.5
voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] Measured 4068.78 5082.18 1013.4
347 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Rooted 0 32.3671 31.1453 1.2218
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Measured Divided 1491.75 1591.6 1.06693
carboxypeptidase h precursor (ec 3.4.17.10) (cph) (carboxypeptidase e) (cpe) (enkephalin convertase) (prohormone processing carboxypeptidase). [swissprot;acc:p16870] Ranked 7670 7311 1.0491
cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] Rooted 1 66.4284 60.0004 1.10713
enteropeptidase precursor (ec 3.4.21.9) (enterokinase). [swissprot;acc:p98073] Measured 4991.02 5885.09 1.17914
gtp:amp phosphotransferase mitochondrial (ec 2.7.4.10) (ak3) (adenylate kinase 3 alpha like 1). [swissprot;acc:q9uij7] Ranked 242.14 265.697 1.09729
hydroxyindole o-methyltransferase (ec 2.1.1.4) (hiomt) (acetylserotonin o-methyltransferase) (asmt). [swissprot;acc:p46597] Squared 0 10717.9 12115.3 1.13038
krueppel-like factor 5 (intestinal-enriched krueppel-like factor) (colon krueppel-like factor) (transcription factor bteb2) (basic transcription element binding protein 2) (bte-binding protein 2) (gc box binding protein 2). [swissprot;acc:q13887] Rooted Subtracted 1 57.9819 64.9302 6.9483
prefoldin subunit 3 (von hippel-lindau binding protein 1) (vhl binding protein-1) (vbp-1) (hibbj46). [swissprot;acc:q15765] Squared 0 20.3193 57.5264 37.2071
scratch; scratch 1. [refseq;acc:nm_031309] Measured 1398.21 1339.9 58.31
Rooted Divided 21.5021 20.4389 1.05202
shroom-related protein; f-actin-binding protein; likely ortholog of mouse shroom. [refseq;acc:nm_020859] Ranked Subtracted 1 231.481 211.131 20.35
small nuclear ribonucleoprotein sm d2 (snrnp core protein d2) (sm-d2). [swissprot;acc:p43330] Squared Divided 16573.6 20637.8 1.24522
swi/snf-related matrix-associated actin-dependent regulator of chromatin c2 isoform a; mammalian chromatin remodeling complex brg1-associated factor 170; chromatin remodeling complex baf170 subunit; swi3-like protein; swi/snf complex 170 kda subunit. [refseq;acc:nm_003075] Ranked Subtracted 0 13247.9 12674.2 573.7
transcription factor btf3 homolog 3. [swissprot;acc:q13892] Squared 1 34268.1 40650.4 6382.3
voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] Measured 4068.82 5082.21 1013.39
348 3-hydroxyisobutyryl-coenzyme a hydrolase. [refseq;acc:nm_014362] Ranked 0 9897.29 10466.5 569.21
ad24 protein. [refseq;acc:nm_022451] Rooted Divided 1 49.2558 54.5235 1.10695
adenylate kinase isoenzyme 4, mitochondrial (ec 2.7.4.3) (atp-amp transphosphorylase). [swissprot;acc:p27144] Ranked 242.14 265.696 1.09728
baculoviral iap repeat-containing protein 5 (apoptosis inhibitor survivin) (apoptosis inhibitor 4). [swissprot;acc:o15392] Measured 0 14357.1 13463.1 1.0664
dj850e9.1 (novel c2h2 type zinc finger protein similar to drosophila scratch (scrt), slug and xenopus snail) (fragment). [sptrembl;acc:q9nq03] Subtracted 1388.29 1330.37 57.92

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/