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 Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 812 to 861 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Value Type
description
red
green
network_comparison
203 Rooted transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 46.3291 53.1063 1.14628
204 Measured small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 4512.19 5655.52 1.25339
Ranked short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 201.515 228.752 1.13516
Squared source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 12326.4 16522.9 1.34045
Rooted small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 55.8956 63.9636 1.14434
205 Measured small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 4512.19 5655.52 1.25339
Ranked luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 228.1 200.968 1.13501
Squared oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 12326.4 16522.9 1.34045
Rooted small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 55.8956 63.9636 1.14434
206 Measured atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 5720.25 4577.5 1.24965
Ranked luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 228.085 201.006 1.13472
Squared dolichyl-diphosphooligosaccharide--protein glycosyltransferase 48 kda subunit precursor (ec 2.4.1.119) (oligosaccharyl transferase 48 kda subunit) (ddost 48 kda subunit). [swissprot;acc:p39656] 12326.4 16522.9 1.34045
Rooted gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 140.508 122.878 1.14348
207 Measured splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 4771.21 5961.43 1.24946
Ranked presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 285.684 252.234 1.13261
Squared solute carrier family 4 (anion exchanger), member 1, adaptor protein; kidney anion exchanger adaptor protein; kanadaptin; lung cancer oncogene 3. [refseq;acc:nm_018158] 70525.9 52678.7 1.33879
Rooted apg3p; pc3-96 protein. [refseq;acc:nm_022488] 140.508 122.878 1.14348
208 Measured voltage-dependent calcium channel gamma-8 subunit (neuronal voltage- gated calcium channel gamma-8 subunit). [swissprot;acc:q8wxs5] 4068.78 5082.18 1.24907
Ranked 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
Squared cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 70525.9 52678.7 1.33879
Rooted atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 46.901 53.624 1.14334
209 Measured voltage-dependent calcium channel gamma-3 subunit (neuronal voltage- gated calcium channel gamma-3 subunit). [swissprot;acc:o60359] 4068.78 5082.18 1.24907
Ranked 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
Squared catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 70525.9 52678.7 1.33879
Rooted calpain 2, large [catalytic] subunit precursor (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (m-type) (m-calpain) (millimolar-calpain) (calpain large polypeptide l2). [swissprot;acc:p17655] 46.8525 53.5324 1.14257
210 Measured voltage-dependent calcium channel gamma-2 subunit (neuronal voltage- gated calcium channel gamma-2 subunit). [swissprot;acc:q9y698] 4068.82 5082.21 1.24906
Ranked cullin homolog 2 (cul-2). [swissprot;acc:q13617] 285.684 252.234 1.13261
Squared small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] 69549 92953.5 1.33652
Rooted calpain 1, large [catalytic] subunit (ec 3.4.22.17) (calcium-activated neutral proteinase) (canp) (mu-type) (mucanp) (micromolar-calpain). [swissprot;acc:p07384] 46.8525 53.5316 1.14256
211 Measured voltage-dependent calcium channel gamma-4 subunit (neuronal voltage- gated calcium channel gamma-4 subunit). [swissprot;acc:q9ubn1] 4068.91 5082.27 1.24905
Ranked presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 285.684 252.234 1.13261
Squared nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 14668.3 19547 1.3326
Rooted metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 88.4361 77.5112 1.14095
212 Measured transcription factor iiib 90 kda subunit (tfiiib90) (htfiiib90) (b- related factor 1) (hbrf) (tata box-binding protein-associated factor, rna polymerase iii, subunit 2) (taf3b2). [swissprot;acc:q92994] 4446.72 5553.79 1.24896
Ranked cullin homolog 1 (cul-1). [swissprot;acc:q13616] 285.684 252.234 1.13261
Squared nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 14690.3 19560.2 1.3315
Rooted beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 88.4266 77.5047 1.14092
213 Measured nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 4446.72 5553.79 1.24896
Ranked pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 210.693 186.95 1.127
Squared signal transducing adaptor molecule 1; signal transducing adaptor molecule. [refseq;acc:nm_003473] 86861.5 65369.7 1.32877
Rooted associated molecule with the sh3 domain of stam (amsh) like protein. [refseq;acc:nm_020799] 105.205 92.2415 1.14054
214 Measured voltage-dependent calcium channel gamma-5 subunit (neuronal voltage- gated calcium channel gamma-5 subunit). [swissprot;acc:q9uf02] 4074.83 5086.49 1.24827
Ranked lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] 191.644 170.192 1.12605
Squared trna (5-methylaminomethyl-2-thiouridylate)-methyltransferase (ec 2.1.1.61). [swissprot;acc:o75648] 52591.3 69845.1 1.32807
Rooted putative breast adenocarcinoma marker (32kd). [refseq;acc:nm_014453] 105.205 92.2415 1.14054
215 Measured transforming protein p21a (k-ras 2a) (ki-ras) (c-k-ras). [swissprot;acc:p01116] 16074 12888.4 1.24717
Ranked myosin heavy chain, cardiac muscle alpha isoform (myhc-alpha). [swissprot;acc:p13533] 112 126 1.125
Squared protein kinase c, eta type (ec 2.7.1.-) (npkc-eta) (pkc-l). [swissprot;acc:p24723] 86609.4 65234.5 1.32766
Rooted associated molecule with the sh3 domain of stam. [refseq;acc:nm_006463] 105.205 92.2415 1.14054
216 Measured leucine-rich repeat protein shoc-2 (ras-binding protein sur-8). [swissprot;acc:q9uq13] 16071.6 12886.8 1.24714

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/