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.


Navigation/Query Panel:
Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
Gene Rank expected description measured Hugo final
Results: HTML CSV LaTeX Showing element 2402 to 2451 of 3206 in total
Rank
expected
description
measured
Hugo
final
2402 0.392545 WILLIAMS BEUREN SYNDROME CHROMOSOME REGION 20C ISOFORM 1. [RefSeq;Acc:NM_032158] 0.0859883 NSUN5B 0.219053357
2403 1.22481 PROHIBITIN. [SWISSPROT;Acc:P35232] 0.26817 PHB 0.218948245
2404 REPRESSOR OF ESTROGEN RECEPTOR ACTIVITY; B-CELL ASSOCIATED PROTEIN. [RefSeq;Acc:NM_007273] no value
2405 0.115441 INTEGRAL MEMBRANE PROTEIN 2A (E25 PROTEIN). [SWISSPROT;Acc:O43736] 0.0252512 ITM2A 0.218736844
2406 0.117061 INTEGRAL MEMBRANE PROTEIN 2C (TRANSMEMBRANE PROTEIN BRI3) (NPD018). [SWISSPROT;Acc:Q9NQX7] 0.0256055 ITM2C 0.218736385
2407 0.140868 INTEGRAL MEMBRANE PROTEIN 2B (TRANSMEMBRANE PROTEIN BRI) [CONTAINS: ABRI/ADAN AMYLOID PEPTIDE]. [SWISSPROT;Acc:Q9Y287] 0.0308129 ITM2B 0.21873598
2408 0.845209 0.184877 APIP 0.218735248
2409 0.514239 0.112482 no value 0.218734868
2410 0.111754 0.0244129 VPS8 0.218452136
2411 1.3266 TRANSCRIPTION FACTOR SMIF; DECAPPING ENZYME HDCP1A. [RefSeq;Acc:NM_018403] 0.289798 DCP1A 0.218451681
2412 1.63578 PUTATIVE N6-DNA-METHYLTRANSFERASE (EC 2.1.1.-) (PROTEIN PRED28) (M.HSAHEMK2P). [SWISSPROT;Acc:Q9Y5N5] 0.357172 N6AMT1 0.218349656
2413 0.141189 0.030828500000000002 no value 0.218349163
2414 0.114139 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 2. [RefSeq;Acc:NM_178865] 0.0249219 SERINC2 0.218346928
2415 0.136653 TUMOR DIFFERENTIALLY EXPRESSED PROTEIN 1 (TRANSMEMBRANE PROTEIN SBBI99). [SWISSPROT;Acc:Q13530] 0.0298377 SERINC3 0.218346469
2416 HOMOLOG OF YEAST MAF1. [RefSeq;Acc:NM_032272] MAF1
2417 0.118068 TUMOR DIFFERENTIALLY EXPRESSED 1 PROTEIN LIKE. [SWISSPROT;Acc:Q9NRX5] 0.0257797 SERINC1 0.218346207
2418 2.24292 D-3-PHOSPHOGLYCERATE DEHYDROGENASE (EC 1.1.1.95) (3-PGDH). [SWISSPROT;Acc:O43175] 0.489733 PHGDH 0.218346174
2419 0.669424 GENERAL CONTROL OF AMINO ACID SYNTHESIS PROTEIN 5-LIKE 2 (EC 2.3.1.-) (HISTONE ACETYLTRANSFERASE GCN5) (HSGCN5). [SWISSPROT;Acc:Q92830] 0.146069 GCN5L2 0.218201021
2420 0.742662 P300/CBP-ASSOCIATED FACTOR (EC 2.3.1.-) (P/CAF) (HISTONE ACETYLASE PCAF). [SWISSPROT;Acc:Q92831] 0.162045 PCAF 0.218194818
2421 1.96674 FIP1-LIKE 1; REARRANGED IN HYPEREOSINOPHILIA. [RefSeq;Acc:NM_030917] 0.429115 FIP1L1 0.218185932
2422 0.258811 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 2 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 2) (TESTIS-SPECIFIC S-II) (TRANSCRIPTION ELONGATION FACTOR TFIIS.L). [SWISSPROT;Acc:Q15560] 0.0564551 TCEA2 0.218132537
2423 0.29203 TRANSCRIPTION ELONGATION FACTOR A PROTEIN 1 (TRANSCRIPTION ELONGATION FACTOR S-II PROTEIN 1) (TRANSCRIPTION ELONGATION FACTOR TFIIS.O). [SWISSPROT;Acc:P23193] 0.0637011 no value 0.218132041
2424 0.167562 ATP-DEPENDENT DNA HELICASE Q5 (RECQ PROTEIN-LIKE 5) (RECQ5). [SWISSPROT;Acc:O94762] 0.0365106 RECQL5 0.217893078
2425 0.335124 DNA-REPAIR PROTEIN XRCC3 (X-RAY REPAIR CROSS-COMPLEMENTING PROTEIN 3). [SWISSPROT;Acc:O43542] 0.0730211 XRCC3 0.21789278
2426 0.670248 GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE (EC 1.1.1.49) (G6PD). [SWISSPROT;Acc:P11413] 0.146042 G6PD 0.217892482
2427 1.06471 MITOGEN-ACTIVATED PROTEIN KINASE KINASE KINASE 7 (EC 2.7.1.-) (TRANSFORMING GROWTH FACTOR-BETA-ACTIVATED KINASE 1) (TGF-BETA- ACTIVATED KINASE 1). [SWISSPROT;Acc:O43318] 0.231972 MAP3K7 0.217873412
2428 0.672152 PHOSPHOLIPASE D2 (EC 3.1.4.4) (PLD 2) (CHOLINE PHOSPHATASE 2) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D2) (PLD1C) (HPLD2). [SWISSPROT;Acc:O14939] 0.146403 PLD2 0.21781234
2429 0.816721 PHOSPHOLIPASE D1 (EC 3.1.4.4) (PLD 1) (CHOLINE PHOSPHATASE 1) (PHOSPHATIDYLCHOLINE-HYDROLYZING PHOSPHOLIPASE D1) (HPLD1). [SWISSPROT;Acc:Q13393] 0.177815 PLD1 0.217718168
2430 0.429323 SIPL PROTEIN. [RefSeq;Acc:NM_018269] 0.0933761 ADI1 0.217496151
2431 0.657687 FIBULIN-1 PRECURSOR. [SWISSPROT;Acc:P23142] 0.143043 FBLN1 0.217494036
2432 0.452567 0.098396 THNSL1 0.217417532
2433 0.884993 0.192282 IMMP1L 0.217269515
2434 0.725721 IMP2 INNER MITOCHONDRIAL MEMBRANE PROTEASE-LIKE; INNER MITOCHONDRIAL MEMBRANE PEPTIDASE 2 LIKE. [RefSeq;Acc:NM_032549] 0.157677 IMMP2L 0.217269447
2435 MICROSOMAL SIGNAL PEPTIDASE 18 KDA SUBUNIT (EC 3.4.-.-) (SPASE 18 KDA SUBUNIT) (SPC18) (ENDOPEPTIDASE SP18). [SWISSPROT;Acc:P21378] no value
2436 0.159272 0.0346049 SETD3 0.2172692
2437 0.788327 ANAPHASE-PROMOTING COMPLEX SUBUNIT 2; ANAPHASE-PROMOTING COMPLEX 2. [RefSeq;Acc:NM_013366] 0.171257 ANAPC2 0.217241069
2438 0.563645 MY016 PROTEIN. [SPTREMBL;Acc:Q9H3K6] 0.12244 BOLA2B 0.21722893
2439 1.22405 GERANYLGERANYL PYROPHOSPHATE SYNTHETASE (GGPP SYNTHETASE) (GGPPSASE) (GERANYLGERANYL DIPHOSPHATE SYNTHASE) [INCLUDES: DIMETHYLALLYLTRANSFERASE (EC 2.5.1.1); GERANYLTRANSTRANSFERASE (EC 2.5.1.10); FARNESYLTRANSTRANSFERASE (EC 2.5.1.29)]. [SWISSPROT; 0.265861 GGPS1 0.217197827
2440 2.33574 HISTIDYL-TRNA SYNTHETASE (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE) (HISRS). [SWISSPROT;Acc:P12081] 0.507204 HARS 0.217149169
2441 0.178742 MYO-INOSITOL 1-PHOSPHATE SYNTHASE A1. [RefSeq;Acc:NM_016368] 0.0388043 no value 0.217096709
2442 UBIQUITIN-LIKE PROTEIN GDX (UBIQUITIN-LIKE PROTEIN 4). [SWISSPROT;Acc:P11441] UBL4A
2443 2.48653 ARSENICAL PUMP-DRIVING ATPASE (EC 3.6.3.16) (ARSENITE-TRANSLOCATING ATPASE) (ARSENICAL RESISTANCE ATPASE) (ARSENITE-TRANSPORTING ATPASE) (ARSA) (ASNA-I). [SWISSPROT;Acc:O43681] 0.539817 no value 0.217096516
2444 0.536227 0.116413 C7orf20 0.217096491
2445 0.14496 0.0314703 UBL4B 0.21709644
2446 0.502445 LARGE PROLINE-RICH PROTEIN BAT3 (HLA-B-ASSOCIATED TRANSCRIPT 3) (G3). [SWISSPROT;Acc:P46379] 0.109079 no value 0.217096399
2447 2.0418 HISTIDYL-TRNA SYNTHETASE HOMOLOG (EC 6.1.1.21) (HISTIDINE--TRNA LIGASE HOMOLOG) (HISRS). [SWISSPROT;Acc:P49590] 0.443267 HARS2 0.21709619
2448 0.94731 CAAX PRENYL PROTEASE 1 HOMOLOG (EC 3.4.24.-) (PRENYL PROTEIN-SPECIFIC ENDOPROTEASE 1) (FARNESYLATED-PROTEINS CONVERTING ENZYME 1) (FACE-1) (ZINC METALLOPROTEINASE STE24 HOMOLOG). [SWISSPROT;Acc:O75844] 0.205647 ZMPSTE24 0.21708522
2449 0.345603 6-PHOSPHOGLUCONOLACTONASE (EC 3.1.1.31) (6PGL). [SWISSPROT;Acc:O95336] 0.0750119 PGLS 0.217046438
2450 0.808504 0.175357 HDHD3 0.216890702
2451 E-1 ENZYME. [RefSeq;Acc:NM_021204] ENOPH1

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/