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 Network Type I Analysis

Type 1 network in which we propagated the absolute log regulation ratio abs(log(r/g)). We used the filtered lowest boundary of the confidence interval for the microarray measurement based and used the high confidence interaction map. Because type-I networks tend to favour highly connected proteins we tested a normalisation scheme in which we would run the network once with real values (the measured column) and once with simulated values where each measured point is set to 1 instead of the actual signal (the expected column). Afterwards we divided the measured value by the expected value. This normalisation scheme works to a certain extend but will lead to a variance that is directly related to the connectivity of each protein. In the end we dropped the use of Type-I networks due to the many technical problems they pose.


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expected Gene Rank measured Hugo description final
Results: HTML CSV LaTeX Showing element 2052 to 2101 of 3206 in total
expected
Rank
measured
Hugo
description
final
0.814576 650 0.218174 MAPK8IP3 C-JUN-AMINO-TERMINAL KINASE INTERACTING PROTEIN 3 (JNK-INTERACTING PROTEIN 3) (JIP-3) (JNK MAP KINASE SCAFFOLD PROTEIN 3) (MITOGEN- ACTIVATED PROTEIN KINASE 8-INTERACTING PROTEIN 3). [SWISSPROT;Acc:Q9UPT6] 0.267837501
0.814661 2504 0.174979 AZIN1 ORNITHINE DECARBOXYLASE ANTIZYME INHIBITOR. [SWISSPROT;Acc:O14977] 0.214787501
0.815319 341 0.232195 RBBP4 CHROMATIN ASSEMBLY FACTOR 1 SUBUNIT C (CAF-1 SUBUNIT C) (CHROMATIN ASSEMBLY FACTOR I P48 SUBUNIT) (CAF-I 48 KDA SUBUNIT) (CAF-IP48) (RETINOBLASTOMA BINDING PROTEIN P48) (RETINOBLASTOMA-BINDING PROTEIN 4) (RBBP-4) (MSI1 PROTEIN HOMOLOG). [SWISSPROT; 0.28479037
0.816035 3102 0.0752577 NEUROD1 NEUROGENIC DIFFERENTIATION FACTOR 1 (NEUROD1) (NEUROD). [SWISSPROT;Acc:Q13562] 0.092223618
0.8167 2564 0.174535 GLUL GLUTAMINE SYNTHETASE (EC 6.3.1.2) (GLUTAMATE--AMMONIA LIGASE). [SWISSPROT;Acc:P15104] 0.213707604
0.816721 2429 0.177815 PLD1 PHOSPHOLIPASE D1 (EC 3.1.4.4) (PLD 1) (CHOLINE PHOSPHATASE 1) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D1) (HPLD1). [SWISSPROT;Acc:Q13393] 0.217718168
0.816964 746 0.216085 EIF3K EUKARYOTIC TRANSLATION INITIATION FACTOR 3 SUBUNIT 11 (EIF-3 P25) (EIF3K) (MUSCLE SPECIFIC GENE M9 PROTEIN) (PTD001) (HSPC029) (ARG134). [SWISSPROT;Acc:Q9UBQ5] 0.264497579
0.818 2847 0.156536 JPH2 JUNCTOPHILIN 2 (JUNCTOPHILIN TYPE 2) (JP-2). [SWISSPROT;Acc:Q9BR39] 0.191364303
0.818463 1310 0.201117 HUS1 HUS1 CHECKPOINT PROTEIN; HUS1 (S. POMBE) CHECKPOINT HOMOLOG; HUS1+-LIKE PROTEIN. [RefSeq;Acc:NM_004507] 0.245725219
0.818777 955 0.209882 PTPRA VACUOLAR PROTEIN SORTING 16 (HVPS16). [SWISSPROT;Acc:Q9H269] 0.256335974
0.819215 481 0.224714 ARF3 ADP-RIBOSYLATION FACTOR 3. [SWISSPROT;Acc:P16587] 0.274304059
0.8195 2848 0.156823 JPH3 JUNCTOPHILIN 3 (JUNCTOPHILIN TYPE 3) (JP-3). [SWISSPROT;Acc:Q8WXH2] 0.191364246
0.819994 1380 0.200609 BAG1 BAG-FAMILY MOLECULAR CHAPERONE REGULATOR-1 (BCL-2 BINDING ATHANOGENE- 1) (BAG-1) (GLUCOCORTICOID RECEPTOR-ASSOCIATED PROTEIN RAP46). [SWISSPROT;Acc:Q99933] 0.244646912
0.820367 3174 0.0455028 NXF5 NUCLEAR RNA EXPORT FACTOR 5 (TAP-LIKE PROTEIN 1) (TAPL-1). [SWISSPROT;Acc:Q9H1B4] 0.055466395
0.821038 1691 0.195442 NADK PUTATIVE INORGANIC POLYPHOSPHATE/ATP-NAD KINASE (EC 2.7.1.23) (POLY(P)/ATP NAD KINASE). [SWISSPROT;Acc:O95544] 0.238042575
0.821543 2828 0.158934 ZNF174 ZINC FINGER PROTEIN 174 (AW-1). [SWISSPROT;Acc:Q15697] 0.19345792
0.821874 897 0.21331 VPS18 VACUOLAR PROTEIN SORTING 18 (HVPS18). [SWISSPROT;Acc:Q9P253] 0.259541
0.82204 2318 0.18235 PMM2 PHOSPHOMANNOMUTASE 2 (EC 5.4.2.8) (PMM 2). [SWISSPROT;Acc:O15305] 0.221826189
0.822334 2893 0.144225 LASS5 0.175384941
0.822563 2274 0.183185 MTRF1L MITOCHONDRIAL TRANSLATIONAL RELEASE FACTOR 1-LIKE. [RefSeq;Acc:NM_019041] 0.222700267
0.824492 235 0.259541 POLE "DNA POLYMERASE EPSILON, CATALYTIC SUBUNIT A (EC 2.7.7.7) (DNA POLYMERASE II SUBUNIT A). [SWISSPROT;Acc:Q07864]" 0.314788985
0.824699 617 0.221484 PPP3CC "SERINE/THREONINE PROTEIN PHOSPHATASE 2B CATALYTIC SUBUNIT, GAMMA ISOFORM (EC 3.1.3.16) (CALMODULIN-DEPENDENT CALCINEURIN A SUBUNIT, GAMMA ISOFORM) (CALCINEURIN, TESTIS-SPECIFIC CATALYTIC SUBUNIT) (CAM-PRP CATALYTIC SUBUNIT). [SWISSPROT;Acc:P48454]" 0.26856344
0.825859 761 0.217793 DVL1 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-1 (DISHEVELLED-1) (DSH HOMOLOG 1). [SWISSPROT;Acc:O14640] 0.26371693
0.826637 133 0.290469 GABRG3 GAMMA-AMINOBUTYRIC-ACID RECEPTOR GAMMA-3 SUBUNIT PRECURSOR (GABA(A) RECEPTOR). [SWISSPROT;Acc:Q99928] 0.351386401
134 no value INTERLEUKIN-1 RECEPTOR-ASSOCIATED KINASE 4; INTERLEUKIN-1 RECEPTOR ASSOCIATED KINASE 4. [RefSeq;Acc:NM_016123]
135 FOXG1 FORKHEAD BOX PROTEIN G1C (FORKHEAD-RELATED PROTEIN FKHL3) (HFK3) (FRAGMENT). [SWISSPROT;Acc:Q14488]
136 JMJD6 PHOSPHATIDYLSERINE RECEPTOR; PHOSPHATIDYLSERINE RECEPTOR BETA. [RefSeq;Acc:NM_015167]
0.827018 3107 0.0762705 CHD5 CHROMODOMAIN HELICASE DNA BINDING PROTEIN 5. [RefSeq;Acc:NM_015557] 0.092223507
0.827431 2505 0.177719 ADC ORNITHINE DECARBOXYLASE-LIKE PROTEIN (EC 4.1.1.17) (ODC-PARALOGUE) (ODC-P). [SWISSPROT;Acc:Q96A70] 0.214784073
0.827963 1834 0.193647 C15orf15 RIBOSOMAL PROTEIN L24-LIKE; 60S RIBOSOMAL PROTEIN L30 ISOLOG; MY024 PROTEIN; HOMOLOG OF YEAST RIBOSOMAL LIKE PROTEIN 24. [RefSeq;Acc:NM_016304] 0.23388364
0.828397 2312 0.183942 AP3M2 ADAPTER-RELATED PROTEIN COMPLEX 3 MU 2 SUBUNIT (CLATHRIN COAT ASSEMBLY PROTEIN AP47 HOMOLOG 2) (CLATHRIN COAT ASSOCIATED PROTEIN AP47 HOMOLOG 2) (GOLGI ADAPTOR AP-1 47 KDA PROTEIN HOMOLOG 2) (HA1 47 KDA SUBUNIT HOMOLOG 2) (CLATHRIN ASSEMBLY PROTEIN ASSEMB 0.22204571
0.828592 1924 0.192198 POLR3C POLYMERASE (RNA) III (DNA DIRECTED) (62KD). [RefSeq;Acc:NM_006468] 0.231957345
0.828912 2379 0.18221 HLCS BIOTIN--PROTEIN LIGASE (EC 6.3.4.-) (BIOTIN APO-PROTEIN LIGASE) [INCLUDES: BIOTIN--[METHYLMALONYL-COA-CARBOXYLTRANSFERASE] LIGASE (EC 6.3.4.9); BIOTIN--[PROPIONYL-COA-CARBOXYLASE [ATP-HYDROLYZING]] LIGASE (EC 6.3.4.10) (HOLOCARBOXYLASE SYNTHETASE) (HCS); 0.219818268
0.830447 2856 0.158456 TPI1 TRIOSEPHOSPHATE ISOMERASE (EC 5.3.1.1) (TIM). [SWISSPROT;Acc:P00938] 0.190808083
0.830799 706 0.220284 AOF2 0.265147166
0.831867 1006 0.211877 NR2C1 ORPHAN NUCLEAR RECEPTOR TR2. [SWISSPROT;Acc:P13056] 0.254700571
0.832 1555 0.200816 PAICS MULTIFUNCTIONAL PROTEIN ADE2 [INCLUDES: PHOSPHORIBOSYLAMINOIMIDAZOLE- SUCCINOCARBOXAMIDE SYNTHASE (EC 6.3.2.6) (SAICAR SYNTHETASE); PHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE (EC 4.1.1.21) (AIR CARBOXYLASE) (AIRC)]. [SWISSPROT;Acc:P22234] 0.241365385
0.833576 2827 0.161283 no value ZINC FINGER IMPRINTED 2. [SWISSPROT;Acc:Q9NZV7] 0.193483258
0.834222 3186 0.0311291 FCN2 FICOLIN 2 PRECURSOR (COLLAGEN/FIBRINOGEN DOMAIN-CONTAINING PROTEIN 2) (FICOLIN-B) (FICOLIN B) (SERUM LECTIN P35) (EBP-37) (HUCOLIN) (L- FICOLIN). [SWISSPROT;Acc:Q15485] 0.037315127
0.83446 445 0.230886 GSTT1 GLUTATHIONE S-TRANSFERASE THETA 1 (EC 2.5.1.18) (GST CLASS-THETA) (GLUTATHIONE TRANSFERASE T1-1). [SWISSPROT;Acc:P30711] 0.276689116
0.834941 157 0.293028 NCBP2L DJ820B18.1 (SIMILAR TO NUCLEAR CAP BINDING PROTEIN) (FRAGMENT). [SPTREMBL;Acc:Q8WWK2] 0.350956535
0.834998 1280 0.205692 CALR CALRETICULIN PRECURSOR (CRP55) (CALREGULIN) (HACBP) (ERP60). [SWISSPROT;Acc:P27797] 0.246338315
0.836397 3118 0.0737653 SHCBP1 LIKELY ORTHOLOG OF MOUSE SHC SH2-DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_024745] 0.088194123
0.837663 330 0.238906 MYCN N-MYC PROTO-ONCOGENE PROTEIN. [SWISSPROT;Acc:P04198] 0.285205387
0.842838 2685 0.175589 RTN2 RETICULON PROTEIN 2 (NEUROENDOCRINE-SPECIFIC PROTEIN-LIKE 1) (NSP-LIKE PROTEIN 1) (NSPLI). [SWISSPROT;Acc:O75298] 0.208330664
0.843068 606 0.226785 CRX CONE-ROD HOMEOBOX PROTEIN. [SWISSPROT;Acc:O43186] 0.268999654
0.844371 2323 0.187278 RPS21 40S RIBOSOMAL PROTEIN S21. [SWISSPROT;Acc:P35265] 0.221795869
0.84475 2188 0.19122 C12orf65 0.226362829
0.845209 2408 0.184877 APIP 0.218735248
0.846393 762 0.223153 DVL2 SEGMENT POLARITY PROTEIN DISHEVELLED HOMOLOG DVL-2 (DISHEVELLED-2) (DSH HOMOLOG 2). [SWISSPROT;Acc:O14641] 0.263651755

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 bloody hugo identifier as demanded by the BMC Bioinformatics idiots
- http://analysis.yellowcouch.org/