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 Hugo Value Type description Network Comparison Type Interaction Map Filtered red green network_comparison
Results: HTML CSV LaTeX Showing element 801 to 850 of 12912 in total
Network Comparison Type  : Divided
Interaction Map  : High confidence
Filtered  : 1
Rank
Hugo
Value Type
description
red
green
network_comparison
201 CCT4 Measured t-complex protein 1, delta subunit (tcp-1-delta) (cct-delta) (stimulator of tar rna binding). [swissprot;acc:p50991] 4810.22 6075.04 1.26294
CLSTN2 Squared calsyntenin-2 precursor. [swissprot;acc:q9h4d0] 71033.4 95440.2 1.3436
DDOST Rooted 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] 61.2893 70.3856 1.14842
SF4 Ranked splicing factor 4 isoform b; rna-binding protein. [refseq;acc:nm_021164] 240.133 211.382 1.13601
202 no value Rooted splicing factor 3b subunit 3 (spliceosome associated protein 130) (sap 130) (sf3b130) (pre-mrna splicing factor sf3b 130 kda subunit). [swissprot;acc:q15393] 57.3527 65.7973 1.14724
CLSTN3 Squared calsyntenin-3 precursor. [swissprot;acc:q9bqt9] 71030.1 95434.8 1.34358
NEDD9 Measured enhancer of filamentation 1 (hef1) (crk-associated substrate-related protein) (cas-l) (casl) (pp105) (neural precursor cell expressed developmentally down-regulated 9). [swissprot;acc:q14511] 4812.01 6076.09 1.26269
TRPC4 Ranked short transient receptor potential channel 4 (trpc4) (trp-related protein 4) (htrp-4) (htrp4). [swissprot;acc:q9ubn4] 201.478 228.784 1.13553
203 no value Squared hpaii tiny fragments locus 9c. [refseq;acc:nm_022727] 20988.2 15632.1 1.34263
Rooted transcription factor dp-1 (e2f dimerization partner 1) (drtf1- polypeptide-1) (drtf1). [swissprot;acc:q14186] 46.3291 53.1063 1.14628
ATG12 Measured autophagy protein 12-like (apg12-like). [swissprot;acc:o94817] 11757.8 9352.11 1.25723
TBC1D10A Ranked ebp50-pdz interactor of 64 kda (epi64 protein). [swissprot;acc:q9bxi6] 201.515 228.752 1.13516
204 no value Measured small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [swissprot;acc:p08578] 4512.19 5655.52 1.25339
Rooted 55.8956 63.9636 1.14434
STT3B Squared source of immunodominant mhc-associated peptides; homolog of yeast stt3 gene. [refseq;acc:nm_178862] 12326.4 16522.9 1.34045
TRPC5 Ranked short transient receptor potential channel 5 (trpc5) (htrp-5) (htrp5). [swissprot;acc:q9ul62] 201.515 228.752 1.13516
205 LUC7L2 luc7-like 2; cgi-74 protein; cgi-59 protein. [refseq;acc:nm_016019] 228.1 200.968 1.13501
SNRPF Measured small nuclear ribonucleoprotein f (snrnp-f) (sm protein f) (sm-f) (smf). [swissprot;acc:q15356] 4512.19 5655.52 1.25339
Rooted 55.8956 63.9636 1.14434
STT3A Squared oligosaccharyl transferase stt3 subunit homolog (b5) (integral membrane protein 1) (tmc). [swissprot;acc:p46977] 12326.4 16522.9 1.34045
206 no value Measured atlastin; guanylate-binding protein 3. [refseq;acc:nm_015915] 5720.25 4577.5 1.24965
Rooted gaba-a receptor-associated protein. [sptrembl;acc:q9by60] 140.508 122.878 1.14348
DDOST 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
LUC7L Ranked luc7-like; sarcoplasmic reticulum protein luc7b1. [refseq;acc:nm_018032] 228.085 201.006 1.13472
207 no value 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
ATG3 Rooted apg3p; pc3-96 protein. [refseq;acc:nm_022488] 140.508 122.878 1.14348
PSEN2 Ranked presenilin 2 (ps-2) (stm-2) (e5-1) (ad3lp) (ad5). [swissprot;acc:p49810] 285.684 252.234 1.13261
SLC4A1AP 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
208 CACNG8 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
CKS2 Squared cyclin-dependent kinases regulatory subunit 2 (cks-2). [swissprot;acc:p33552] 70525.9 52678.7 1.33879
DDX24 Rooted atp-dependent rna helicase ddx24 (dead-box protein 24). [swissprot;acc:q9gzr7] 46.901 53.624 1.14334
SKP1A 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
209 CACNG3 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
CAPN2 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
CTNNAL1 Squared catenin (cadherin-associated protein), alpha-like 1; alpha-catulin. [refseq;acc:nm_003798] 70525.9 52678.7 1.33879
FBXW7 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
210 CACNG2 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
CAPN1 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
CUL2 Ranked cullin homolog 2 (cul-2). [swissprot;acc:q13617] 285.684 252.234 1.13261
SGTA Squared small glutamine-rich tetratricopeptide repeat-containing protein (vpu-binding protein) (ubp). [swissprot;acc:o43765] 69549 92953.5 1.33652
211 CACNG4 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
PITRM1 Rooted metalloprotease 1; metalloprotease 1 (pitrilysin family). [refseq;acc:nm_014889] 88.4361 77.5112 1.14095
PSEN1 Ranked presenilin 1 (ps-1) (s182 protein). [swissprot;acc:p49768] 285.684 252.234 1.13261
TIA1 Squared nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] 14668.3 19547 1.3326
212 ALG1 Rooted beta-1,4 mannosyltransferase. [refseq;acc:nm_019109] 88.4266 77.5047 1.14092
BRF1 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
CUL1 Ranked cullin homolog 1 (cul-1). [swissprot;acc:q13616] 285.684 252.234 1.13261
TIAL1 Squared nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] 14690.3 19560.2 1.3315
213 NOLA1 Measured nucleolar protein family a, member 1; gar1 protein. [refseq;acc:nm_018983] 4446.72 5553.79 1.24896
PLDN Ranked pallidin; pallid (mouse) homolog, pallidin. [refseq;acc:nm_012388] 210.693 186.95 1.127

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
- Hugo is the HGNC identifier if it exists
- 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/