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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Hugo measured Gene Rank description expected final
Results: HTML CSV LaTeX Showing element 2658 to 2707 of 3206 in total
Hugo
measured
Rank
description
expected
final
SGTA 0.897082 2815 SMALL GLUTAMINE-RICH TETRATRICOPEPTIDE REPEAT-CONTAINING PROTEIN (VPU-BINDING PROTEIN) (UBP). [SWISSPROT;Acc:O43765] 4.61021 0.19458593
SH2D3C 0.122271 187 SH2 DOMAIN CONTAINING 3C; NOVEL SH2-CONTAINING PROTEIN 3; SH2 DOMAIN-CONTAINING 3C; LIKELY ORTHOLOG OF MOUSE CAS/HEF1-ASSOCIATED SIGNAL TRANSDUCER. [RefSeq;Acc:NM_005489] 0.37176 0.328897676
SH3BGR 0.046789 549 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH PROTEIN (SH3BGR PROTEIN) (21- GLUTAMIC ACID-RICH PROTEIN) (21-GARP). [SWISSPROT;Acc:P55822] 0.172653 0.271000214
SH3BGRL 0.0371738 556 SH3 DOMAIN-BINDING GLUTAMIC ACID-RICH-LIKE PROTEIN. [SWISSPROT;Acc:O75368] 0.137173 0.270999395
SH3GL1 0.172401 2501 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] 0.800978 0.215238121
SH3GL2 0.158519 2497 SH3-CONTAINING GRB2-LIKE PROTEIN 2 (SH3 DOMAIN PROTEIN 2A) (ENDOPHILIN 1) (EEN-B1). [SWISSPROT;Acc:Q99962] 0.735941 0.215396343
SH3GL3 0.171407 2493 SH3-CONTAINING GRB2-LIKE PROTEIN 3 (SH3 DOMAIN PROTEIN 2C) (EEN-B2). [SWISSPROT;Acc:Q99963] 0.795244 0.215540136
SHC1 0.0444669 479 SHC TRANSFORMING PROTEIN. [SWISSPROT;Acc:P29353] 0.162108 0.274304168
SHC2 0.0379081 475 PROTEIN SCK (FRAGMENT). [SWISSPROT;Acc:P98077] 0.138197 0.274304797
SHC3 0.0378858 476 NEURONAL SHC. [RefSeq;Acc:NM_016848] 0.138116 0.274304208
SHCBP1 0.0737653 3118 LIKELY ORTHOLOG OF MOUSE SHC SH2-DOMAIN BINDING PROTEIN 1. [RefSeq;Acc:NM_024745] 0.836397 0.088194123
SHMT1 0.494954 1926 "SERINE HYDROXYMETHYLTRANSFERASE, CYTOSOLIC (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34896]" 2.13521 0.231805771
SHMT2 0.413255 1903 "SERINE HYDROXYMETHYLTRANSFERASE, MITOCHONDRIAL PRECURSOR (EC 2.1.2.1) (SERINE METHYLASE) (GLYCINE HYDROXYMETHYLTRANSFERASE) (SHMT). [SWISSPROT;Acc:P34897]" 1.77935 0.232250541
SHOC2 0.100774 2958 LEUCINE-RICH REPEAT PROTEIN SHOC-2 (RAS-BINDING PROTEIN SUR-8). [SWISSPROT;Acc:Q9UQ13] 0.689453 0.146165148
SHQ1 0.0311675 1262 0.126112 0.24714143
SHROOM2 0.117195 88 APICAL-LIKE PROTEIN (APXL PROTEIN). [SWISSPROT;Acc:Q13796] 0.30421 0.385243746
SHROOM3 0.152828 90 SHROOM-RELATED PROTEIN; F-ACTIN-BINDING PROTEIN; LIKELY ORTHOLOG OF MOUSE SHROOM. [RefSeq;Acc:NM_020859] 0.396725 0.385224022
SHROOM4 91
SIAH2 0.454535 474 SEVEN IN ABSENTIA HOMOLOG 2. [RefSeq;Acc:NM_005067] 1.65694 0.274321943
SIM1 0.0318532 1268 SINGLE-MINDED HOMOLOG 1. [SWISSPROT;Acc:P81133] 0.12912 0.246694548
SIN3A 0.0283438 2029 "TRANSCRIPTIONAL CO-REPRESSOR SIN3A; TRANSCRIPTIONAL REGULATOR, SIN3A (YEAST). [RefSeq;Acc:NM_015477]" 0.123075 0.230296973
SIN3B 0.0370628 2027 0.160934 0.230298135
SIP1 0.092033 1477 SURVIVAL OF MOTOR NEURON PROTEIN-INTERACTING PROTEIN 1 (SMN- INTERACTING PROTEIN 1) (COMPONENT OF GEMS 2) (GEMIN2). [SWISSPROT;Acc:O14893] 0.378775 0.242975381
SIPA1L2 0.0814182 687 0.306494 0.265643699
SIPA1L3 0.0644285 692 0.242538 0.26564291
SIRT1 0.0404428 2052 SIRTUIN 1; SIR2-LIKE 1; SIRTUIN TYPE 1; SIR2ALPHA; SIRTUIN SILENT MATING TYPE INFORMATION REGULATION 2 HOMOLOG 1 (S. CEREVISIAE). [RefSeq;Acc:NM_012238] 0.17588 0.229945417
SIX1 0.617064 666 HOMEOBOX PROTEIN SIX1 (SINE OCULIS HOMEOBOX HOMOLOG 1). [SWISSPROT;Acc:Q15475] 2.31135 0.266971251
SIX2 0.516908 663 HOMEOBOX PROTEIN SIX2 (SINE OCULIS HOMEOBOX HOMOLOG 2). [SWISSPROT;Acc:Q9NPC8] 1.93534 0.267088987
SKP1A 0.145007 3178 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). [SWISSPR 2.91316 0.049776531
SLC13A1 0.0481673 2659 "SOLUTE CARRIER FAMILY 13, MEMBER 1 (RENAL SODIUM/SULFATE COTRANSPORTER) (NA(+)/SULFATE COTRANSPORTER) (HNASI-1). [SWISSPROT;Acc:Q9BZW2]" 0.229436 0.209937848
SLC13A2 0.0401827 2660 "SOLUTE CARRIER FAMILY 13, MEMBER 2 (RENAL SODIUM/DICARBOXYLATE COTRANSPORTER) (NA(+)/DICARBOXYLATE COTRANSPORTER 1) (NADC-1). [SWISSPROT;Acc:Q13183]" 0.191403 0.209937671
SLC13A3 0.0395353 2657 "SOLUTE CARRIER FAMILY 13, MEMBER 3 (SODIUM-DEPENDENT HIGH-AFFINITY DICARBOXYLATE TRANSPORTER 2) (NA(+)/DICARBOXYLATE COTRANSPORTER 3) (NADC-3) (HNADC3). [SWISSPROT;Acc:Q8WWT9]" 0.188319 0.209937924
SLC13A4 0.0480531 2658 "SOLUTE CARRIER FAMILY 13, MEMBER 4 (NA+/SULFATE COTRANSPORTER SUT-1). [SWISSPROT;Acc:Q9UKG4]" 0.228892 0.209937875
SLC15A1 0.245451 280 "OLIGOPEPTIDE TRANSPORTER, SMALL INTESTINE ISOFORM (PEPTIDE TRANSPORTER 1) (INTESTINAL H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 1). [SWISSPROT;Acc:P46059]" 0.807655 0.303905752
SLC15A2 0.33474 278 "OLIGOPEPTIDE TRANSPORTER, KIDNEY ISOFORM (PEPTIDE TRANSPORTER 2) (KIDNEY H+/PEPTIDE COTRANSPORTER) (SOLUTE CARRIER FAMILY 15, MEMBER 2). [SWISSPROT;Acc:Q16348]" 1.10122 0.303971958
SLC20A1 0.0465225 2362 "SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 1; GLVR-1; PIT-1; GIBBON APE LEUKEMIA VIRUS RECEPTOR 1. [RefSeq;Acc:NM_005415]" 0.211181 0.220296807
SLC20A2 0.0378408 2363 "SOLUTE CARRIER FAMILY 20 (PHOSPHATE TRANSPORTER), MEMBER 2; GLVR-2; PIT-2; GIBBON APE LEUKEMIA VIRUS RECEPTOR 2; MURINE LEUKEMIA VIRUS, AMPHOTROPIC; RECEPTOR. [RefSeq;Acc:NM_006749]" 0.171772 0.220296672
SLC23A1 0.0444669 478 "SOLUTE CARRIER FAMILY 23, MEMBER 1 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 1) (HSVCT1) (NA(+)/L-ASCORBIC ACID TRANSPORTER 1) (YOLK SAC PERMEASE-LIKE MOLECULE 3). [SWISSPROT;Acc:Q9UHI7]" 0.162108 0.274304168
SLC23A2 0.0377969 482 "SOLUTE CARRIER FAMILY 23, MEMBER 2 (SODIUM-DEPENDENT VITAMIN C TRANSPORTER 2) (HSVCT2) (NA(+)/L-ASCORBIC ACID TRANSPORTER 2) (YOLK SAC PERMEASE-LIKE MOLECULE 2) (NUCLEOBASE TRANSPORTER-LIKE 1 PROTEIN). [SWISSPROT;Acc:Q9UGH3]" 0.137792 0.274304023
SLC25A12 0.0255652 2593 "CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR1 (SOLUTE CARRIER FAMILY 25, MEMBER 12). [SWISSPROT;Acc:O75746]" 0.120086 0.212890762
SLC25A13 0.0223249 2589 "CALCIUM-BINDING MITOCHONDRIAL CARRIER PROTEIN ARALAR2 (SOLUTE CARRIER FAMILY 25, MEMBER 13) (CITRIN). [SWISSPROT;Acc:Q9UJS0]" 0.104865 0.212891813
SLC25A31 0.0256535 1695 0.107847 0.237869389
SLC25A4 0.032514 1693 "ADP,ATP CARRIER PROTEIN, HEART/SKELETAL MUSCLE ISOFORM T1 (ADP/ATP TRANSLOCASE 1) (ADENINE NUCLEOTIDE TRANSLOCATOR 1) (ANT 1). [SWISSPROT;Acc:P12235]" 0.136688 0.237870186
SLC25A43 0.0228794 3041 MITOCHONDRIAL SOLUTE CARRIER PROTEIN. [RefSeq;Acc:NM_145305] 0.208398 0.109787042
SLC25A5 0.032514 1692 "ADP,ATP CARRIER PROTEIN, FIBROBLAST ISOFORM (ADP/ATP TRANSLOCASE 2) (ADENINE NUCLEOTIDE TRANSLOCATOR 2) (ANT 2). [SWISSPROT;Acc:P05141]" 0.136688 0.237870186
SLC25A6 0.0311972 1696 "ADP,ATP CARRIER PROTEIN, LIVER ISOFORM T2 (ADP/ATP TRANSLOCASE 3) (ADENINE NUCLEOTIDE TRANSLOCATOR 3) (ANT 3). [SWISSPROT;Acc:P12236]" 0.131153 0.237868749
SLC27A2 0.553489 2708 VERY-LONG-CHAIN ACYL-COA SYNTHETASE (EC 6.2.1.-) (VERY-LONG-CHAIN- FATTY-ACID-COA LIGASE). [SWISSPROT;Acc:O14975] 2.66927 0.207355944
SLC27A3 0.439273 2715 SOLUTE CARRIER FAMILY 27 MEMBER 3; FATTY ACID TRANSPORT PROTEIN 3. [RefSeq;Acc:NM_024330] 2.11862 0.207339211
SLC27A4 0.416194 2717 "SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 4; FATTY ACID TRANSPORT PROTEIN 4. [RefSeq;Acc:NM_005094]" 2.00736 0.207334011
SLC27A5 0.44721 2714 "SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 5; VERY LONG-CHAIN ACYL-COA SYNTHETASE HOMOLOG 2; VERY LONG-CHAIN ACYL-COA SYNTHETASE-RELATED PROTEIN; LIKELY ORTHOLOG OF MOUSE SOLUTE CARRIER FAMILY 27 (FATTY ACID TRANSPORTER), MEMBER 5. [" 2.15689 0.207340198

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/